Helices in Proteins: Difference between revisions
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This page illustrates the 3 most common helical conformations (among [[Secondary structure|secondary structures]]) found in proteins. | This page illustrates the 3 most common helical conformations (among [[Secondary structure|secondary structures]]) found in proteins. | ||
Each of the three examples below is a decapeptide fragment extracted from actual protein | 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). | ||
<span style="font-size: | <span style="font-size:120%; color:red;"> | ||
<jmol> | <jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<target> | <target>jmol_3</target> | ||
<scriptWhenChecked>set syncMouse on; | <scriptWhenChecked>script applet * @{"set syncMouse on; sync on;"};</scriptWhenChecked> | ||
<scriptWhenUnchecked>sync | <scriptWhenUnchecked>script applet * @{"sync off;"};</scriptWhenUnchecked> | ||
<text>Synchronize the 3 models for rotation with your mouse.</text> | <text>Synchronize the 3 models for rotation with your mouse.</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol></span> | </jmol></span> | ||
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%;"> | ||
| Line 23: | Line 25: | ||
</th> | </th> | ||
</tr> | </tr> | ||
<tr | <tr> | ||
< | <td style="vertical-align:top;text-align:center;"> | ||
<Structure name='jmol_3' load='3L79_514-525.pdb' size='260' scene='Helices_in_Proteins/3_10_helix_start/1' /> | |||
</td> | </td> | ||
<td> | <td style="vertical-align:top;text-align:center;"> | ||
< | <Structure name='jmol_a' load='1HHO_B_5-16.pdb' size='260' scene='Helices_in_Proteins/Alpha_helix_start/1' /> | ||
</td> | </td> | ||
<td> | <td style="vertical-align:top;text-align:center;"> | ||
< | <Structure name='jmol_p' load='2QD3_A_346-357.pdb' size='260' scene='Helices_in_Proteins/Pi_helix_start/3' /> | ||
</td> | </td> | ||
</tr> | </tr> | ||
<tr | <tr> | ||
< | <td style="vertical-align:top;text-align:center;"> | ||
3 | <scene name='Helices_in_Proteins/3_10_helix_start/1' target='jmol_3'>Reset initial display for 3.10</scene> | ||
<br />3 residues/turn | <br />3 residues/turn | ||
<br />rise 0.20 nm/residue | <br />rise 0.20 nm/residue | ||
| Line 42: | Line 44: | ||
<br />H bonds: N<sub>i+3</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+3</sub> → O<sub>i</sub> | ||
<br />φ = -49°, ψ = -26° | <br />φ = -49°, ψ = -26° | ||
<br />[[3l79]]: 514-525 | <br />from [[3l79]]: 514-525 | ||
</td> | </td> | ||
<td> | <td style="vertical-align:top;text-align:center;"> | ||
3.6<sub>13</sub> | <scene name='Helices_in_Proteins/Alpha_helix_start/1' target='jmol_a'>Reset initial display for 3.6<sub>13</sub> (alpha)</scene> | ||
<br />3.6 residues/turn | <br />3.6 residues/turn | ||
<br />rise 0.15 nm/residue | <br />rise 0.15 nm/residue | ||
| Line 51: | Line 53: | ||
<br />H bonds: N<sub>i+4</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+4</sub> → O<sub>i</sub> | ||
<br />φ = -60°, ψ = -45° | <br />φ = -60°, ψ = -45° | ||
<br />1hho chain B: 5-16 | <br />from [[1hho]] chain B: 5-16 | ||
</td> | </td> | ||
<td> | <td style="vertical-align:top;text-align:center;"> | ||
4.4<sub>16</sub> | <scene name='Helices_in_Proteins/Pi_helix_start/3' target='jmol_p'>Reset initial display for 4.4<sub>16</sub> (pi)</scene> | ||
<br />4.4 residues/turn | <br />4.4 residues/turn | ||
<br />rise ~0.115 nm/residue | <br />rise ~0.115 nm/residue | ||
| Line 60: | Line 62: | ||
<br />H bonds: N<sub>i+5</sub> → O<sub>i</sub> | <br />H bonds: N<sub>i+5</sub> → O<sub>i</sub> | ||
<br />φ = -55°, ψ = -70° (approx.) | <br />φ = -55°, ψ = -70° (approx.) | ||
<br />[[2qd3]] chain A: 346-357 | <br />from [[2qd3]] chain A: 346-357 | ||
</td> | </td> | ||
</tr> | </tr> | ||
| Line 66: | Line 68: | ||
</table> | </table> | ||
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. | Change rendering: | ||
<jmol> | |||
<jmolButton> | |||
<target>jmol_3</target> | |||
<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> | |||
<text>backbone - ball and stick</text> | |||
</jmolButton> | |||
<jmolButton> | |||
<target>jmol_3</target> | |||
<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> | |||
<text>backbone and sidechains - ball and stick</text> | |||
</jmolButton> | |||
<jmolButton> | |||
<target>jmol_3</target> | |||
<script>script applet * @{"define temp selected;select not alpha;color bluetint;select protein;wireframe only;wireframe off;cpk 100%;select temp;"};</script> | |||
<text>spacefilling for all</text> | |||
</jmolButton> | |||
<jmolButton> | |||
<target>jmol_3</target> | |||
<script>script applet * @{"define temp selected;select protein;wireframe only;wireframe off;cartoon on;select alpha;cpk 23%;select temp;"};</script> | |||
<text>reset (cartoons)</text> | |||
</jmolButton> | |||
</jmol> | |||
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. | |||
==See Also== | ==See Also== | ||
*[[Basics of Protein Structure]] | |||
*[[Alpha helix]] | |||
*[http://chemapps.stolaf.edu/jmol/jsmol/helix.htm JSmol helix builder] | |||
*[http://wiki.jmol.org/index.php/Recycling_Corner/Alpha_Helix_Generator RIBOZOME - an Alpha Helix Generator] | |||
*[http://en.wikipedia.org/wiki/Alpha_helix Alpha helix] at Wikipedia. | *[http://en.wikipedia.org/wiki/Alpha_helix Alpha helix] at Wikipedia. | ||
*[http://en.wikipedia.org/wiki/310_helix 3-10 helix] at Wikipedia. | |||
*[http://en.wikipedia.org/wiki/Pi_helix Pi helix] at Wikipedia. | |||
*[[Secondary structure]] | *[[Secondary structure]] | ||
*[[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching) | |||
*The same in Spanish: [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación) | |||
==References== | ==References== | ||
<references /> | <references /> | ||
Latest revision as of 14:33, 3 February 2020
Helical conformations in proteinsHelical 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 | ||||||||||||||||||
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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 AlsoSee Also
- Basics of Protein Structure
- Alpha helix
- JSmol helix builder
- RIBOZOME - an Alpha Helix Generator
- Alpha helix at Wikipedia.
- 3-10 helix at Wikipedia.
- Pi helix at Wikipedia.
- Secondary structure
- Protein primary, secondary, tertiary and quaternary structure (slides for teaching)
- The same in Spanish: Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas (en formato de presentación)
ReferencesReferences
- ↑ 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
- ↑ 2.0 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
- ↑ 3.0 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