Helices in Proteins

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==Helical conformations in proteins==
==Helical conformations in proteins==
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This page illustrates the 3 most common helical conformations (secondary structures) found in proteins.
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This page illustrates the 3 most common helical conformations (among [[Secondary structure|secondary structures]]) found in proteins.
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All are decapeptide segments extracted from actual protein structures in the PDB. They are shown using the same scale, for a better comparison.
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Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the [[PDB]]. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled).
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<span style="font-size:120%; color:red;">
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<jmol>
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<jmolCheckbox>
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<target>jmol_3</target>
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<scriptWhenChecked>script applet * @{"set syncMouse on; sync on;"};</scriptWhenChecked>
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<scriptWhenUnchecked>script applet * @{"sync off;"};</scriptWhenUnchecked>
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<text>Synchronize the 3 models for rotation with your mouse.</text>
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</jmolCheckbox>
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</jmol></span>
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To re-align the 3 models, either reload this page or click on each of the 3 green 'Reset' links.
<table style="width:100%;">
<table style="width:100%;">
<tr align="center">
<tr align="center">
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<td style="width:33%;">3<sub>10</sub> helix
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<th style="width:33%;">3<sub>10</sub> helix
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</th>
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<th>alpha helix
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</th>
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<th style="width:33%;">pi helix
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</th>
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</tr>
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<tr>
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<td style="vertical-align:top;text-align:center;">
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<Structure name='jmol_3' load='3L79_514-525.pdb' size='260' scene='Helices_in_Proteins/3_10_helix_start/1' caption='PDB ID [[:Image:3L79_514-525.pdb|3L79_514-525]]' />
</td>
</td>
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<td>alpha helix
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<td style="vertical-align:top;text-align:center;">
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1HHO_B_5-16.pdb
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<Structure name='jmol_a' load='1HHO_B_5-16.pdb' size='260' scene='Helices_in_Proteins/Alpha_helix_start/1' caption='PDB ID [[:Image:1HHO_B_5-16.pdb|1HHO_B_5-16]]' />
</td>
</td>
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<td style="width:33%;">pi helix
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<td style="vertical-align:top;text-align:center;">
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<Structure name='jmol_p' load='2QD3_A_346-357.pdb' size='260' scene='Helices_in_Proteins/Pi_helix_start/3' caption='PDB ID [[:Image:2QD3_A_346-357.pdb|2QD3_A_346-357]]' />
</td>
</td>
</tr>
</tr>
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<tr align="center">
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<tr>
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<td>
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<td style="vertical-align:top;text-align:center;">
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<applet load='1HHO_B_5-16.pdb' size='280' />
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<scene name='Helices_in_Proteins/3_10_helix_start/1' target='jmol_3'>Reset initial display for 3.10</scene>
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<br />3 residues/turn
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<br />rise 0.20 nm/residue
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<br />helix pitch 0.60 nm
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<br />H bonds: N<sub>i+3</sub> &#8594; O<sub>i</sub>
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<br />φ = -49°, ψ = -26°
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<br />from [[3l79]]: 514-525
</td>
</td>
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<td>
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<td style="vertical-align:top;text-align:center;">
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<applet load='1HHO_B_5-16.pdb' size='280' frame='false' />
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<scene name='Helices_in_Proteins/Alpha_helix_start/1' target='jmol_a'>Reset initial display for 3.6<sub>13</sub> (alpha)</scene>
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<br />3.6 residues/turn
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<br />rise 0.15 nm/residue
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<br />helix pitch 0.54 nm
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<br />H bonds: N<sub>i+4</sub> &#8594; O<sub>i</sub>
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<br />φ = -60°, ψ = -45°
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<br />from [[1hho]] chain B: 5-16
</td>
</td>
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<td>
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<td style="vertical-align:top;text-align:center;">
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<applet load='1HHO_B_5-16.pdb' size='280' />
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<scene name='Helices_in_Proteins/Pi_helix_start/3' target='jmol_p'>Reset initial display for 4.4<sub>16</sub> (pi)</scene>
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<br />4.4 residues/turn
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<br />rise ~0.115 nm/residue
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<br />helix pitch ~0.41 nm
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<br />H bonds: N<sub>i+5</sub> &#8594; O<sub>i</sub>
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<br />φ = -55°, ψ = -70° (approx.)
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<br />from [[2qd3]] chain A: 346-357
</td>
</td>
</tr>
</tr>
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</table>
</table>
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Change rendering:
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<jmol>
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<jmolButton>
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<target>jmol_3</target>
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<script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;select backbone;cpk 23%;wireframe 0.15;select temp;"};</script>
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<text>backbone - ball and stick</text>
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</jmolButton>
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<jmolButton>
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<target>jmol_3</target>
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<script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;cpk 23%;wireframe 0.15;select temp;"};</script>
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<text>backbone and sidechains - ball and stick</text>
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</jmolButton>
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<jmolButton>
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<target>jmol_3</target>
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<script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;cpk 100%;select temp;"};</script>
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<text>spacefilling for all</text>
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</jmolButton>
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<jmolButton>
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<target>jmol_3</target>
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<script>script applet * @{"define temp selected;select protein;wireframe only;wireframe off;cartoon on;select alpha;cpk 23%;select temp;"};</script>
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<text>reset (cartoons)</text>
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</jmolButton>
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</jmol>
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The [[alpha helix]] is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids<ref name="novotny">PMID: 15740737</ref><ref name="jourdan">PMID: 12910453</ref><ref name="moradi">PMID: 19923435</ref>. (It is left-handed when formed with D-amino acids<ref name="novotny" /><ref name="jourdan" /><ref name="moradi" />.) When viewed from either end, right-handed helices turn clockwise when followed away from you.
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==See Also==
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*[[Basics of Protein Structure]]
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*[[Alpha helix]]
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*[http://chemapps.stolaf.edu/jmol/jsmol/helix.htm JSmol helix builder]
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*[http://wiki.jmol.org/index.php/Recycling_Corner/Alpha_Helix_Generator RIBOZOME - an Alpha Helix Generator]
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*[http://en.wikipedia.org/wiki/Alpha_helix Alpha helix] at Wikipedia.
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*[http://en.wikipedia.org/wiki/310_helix 3-10 helix] at Wikipedia.
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*[http://en.wikipedia.org/wiki/Pi_helix Pi helix] at Wikipedia.
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*[[Secondary structure]]
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*[[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
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*The same in Spanish: [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentaci&oacute;n)
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==References==
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<references />

Current revision

Helical conformations in proteins

This page illustrates the 3 most common helical conformations (among secondary structures) found in proteins.

Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the PDB. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled).

To re-align the 3 models, either reload this page or click on each of the 3 green 'Reset' links.

310 helix alpha helix pi helix

PDB ID 3L79_514-525

Drag the structure with the mouse to rotate

PDB ID 1HHO_B_5-16

Drag the structure with the mouse to rotate
Drag the structure with the mouse to rotate


3 residues/turn
rise 0.20 nm/residue
helix pitch 0.60 nm
H bonds: Ni+3 → Oi
φ = -49°, ψ = -26°
from 3l79: 514-525


3.6 residues/turn
rise 0.15 nm/residue
helix pitch 0.54 nm
H bonds: Ni+4 → Oi
φ = -60°, ψ = -45°
from 1hho chain B: 5-16


4.4 residues/turn
rise ~0.115 nm/residue
helix pitch ~0.41 nm
H bonds: Ni+5 → Oi
φ = -55°, ψ = -70° (approx.)
from 2qd3 chain A: 346-357

Change rendering:


The alpha helix is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids[1][2][3]. (It is left-handed when formed with D-amino acids[1][2][3].) When viewed from either end, right-handed helices turn clockwise when followed away from you.

See Also

References

  1. ↑ 1.0 1.1 Novotny M, Kleywegt GJ. A survey of left-handed helices in protein structures. J Mol Biol. 2005 Mar 25;347(2):231-41. PMID:15740737 doi:10.1016/j.jmb.2005.01.037
  2. ↑ 2.0 2.1 Jourdan F, Lazzaroni S, Mendez BL, Lo Cantore P, de Julio M, Amodeo P, Iacobellis NS, Evidente A, Motta A. A left-handed alpha-helix containing both L- and D-amino acids: the solution structure of the antimicrobial lipodepsipeptide tolaasin. Proteins. 2003 Sep 1;52(4):534-43. PMID:12910453 doi:http://dx.doi.org/10.1002/prot.10418
  3. ↑ 3.0 3.1 Moradi M, Babin V, Roland C, Darden TA, Sagui C. Conformations and free energy landscapes of polyproline peptides. Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20746-51. Epub 2009 Nov 18. PMID:19923435 doi:10.1073/pnas.0906500106

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