Alpha helix: Difference between revisions
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An <scene name='77/778341/Ballstick/2'>alpha helix</scene> is a type of secondary structure, i.e. a description of how the main chain of a protein is arranged in space. It is a repetitive regular secondary structure (just like the [[beta sheet|beta strand]]), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length. | |||
==Structure, hydrogen bonding and composition== | ==Structure, hydrogen bonding and composition== | ||
<StructureSection load='1hhb' size='400' side='right' caption='alpha helix' scene='77/778341/Ballstick/1'> | <StructureSection load='1hhb' size='400' side='right' caption='alpha helix' scene='77/778341/Ballstick/1'> | ||
In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the <jmol><jmolLink> | In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the <jmol><jmolLink> | ||
<script> select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected; | <script> select 6-14:A and sidechain; spacefill 20%; wireframe 0.3; delay 0.8; select 4-16:A and backbone or 4-16:A.CB; restrict selected; | ||
</script> | </script> | ||
<text>side chains</text> | <text>side chains</text> | ||
</jmolLink></jmol> pointing away from the helical axis. <jmol><jmolLink> | </jmolLink></jmol> pointing away from the helical axis. (Stereo: <jmol><jmolLink> | ||
<script> stereo 5 | <script> stereo 5 | ||
</script> | </script> | ||
<text> | <text>ON</text> | ||
</jmolLink></jmol> In the following, the side chains are truncated at the beta carbon (green) to allow a better view of the main chain. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> (shown as dashed lines) from the <jmol> | </jmolLink></jmol> <jmol><jmolLink> | ||
<script> stereo off | |||
</script> | |||
<text>OFF</text> | |||
</jmolLink></jmol>) In the following, the side chains are truncated at the beta carbon (green) to allow a better view of the main chain. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> (shown as dashed lines) from the <jmol> | |||
<jmolLink> | <jmolLink> | ||
<script> select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4; | <script> select 6-10:A.O; spacefill 30%; delay 0.4; spacefill 20%; delay 0.4; spacefill 30%; delay 0.4; spacefill 20%l delay 0.4; | ||
| Line 60: | Line 64: | ||
==Types of proteins and folds that contain alpha helices== | ==Types of proteins and folds that contain alpha helices== | ||
===Alpha helices in soluble (globular) proteins=== | ===Alpha helices in soluble (globular) proteins=== | ||
The first two protein | The first two protein structures to be determined, [[myoglobin]] and [[hemoglobin]], consist mainly of alpha helices. Researchers were surprised to see how random the orientation of helices seemed to be. Other all alpha-helical proteins show bundles of nearly parallel (or antiparallel) helices (e.g. bacterial cytochrome c' [[1e83]]). In structures that have beta sheets and alpha helices, one common fold is a single beta sheet that is sandwiched by layers of alpha helices on either side (for example [[Carboxypeptidase A]]). When an alpha helix runs along the surface of the protein, one side of it will show polar side chains (solvent accessible) while the other side will show non-polar side chains (part of the hydrophobic core). The alpha helix fits nicely into the major groove of DNA. Many common DNA-binding motifs, such as the helix-turn-helix (e.g. [[FIS protein]]) or the zinc finger motif (e.g. engineered zinc finger protein [[2i13]]), feature a short alpha helix that binds to the major groove of DNA. | ||
===Alpha helices in transmembrane proteins=== | ===Alpha helices in transmembrane proteins=== | ||
A common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid | A common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid receptors that illustrates this fold in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217). | ||
===Alpha helices in coiled coils=== | ===Alpha helices in coiled coils=== | ||
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{What level of structure does an alpha helix refer to?} | {What level of structure does an alpha helix refer to?} | ||
-A. | -A. Primary structure | ||
+B. Secondary structure | +B. Secondary structure | ||
-C. Tertiary structure | -C. Tertiary structure | ||
| Line 117: | Line 121: | ||
</quiz> | </quiz> | ||
==See Also== | |||
* [[Helices in Proteins]]: alpha, 3<sub>10</sub>, and pi helices side by side. | |||
* [[Proteins: primary and secondary structure]] | |||
* [[Secondary structure]] | |||
* [[Protein primary, secondary, tertiary and quaternary structure]] / [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] | |||
* [[Introduction to molecular visualization]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
[[Category:Pages with quizzes]] | [[Category:Pages with quizzes]] | ||