Alpha helix: Difference between revisions

 

In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by <scene name='77/778341/Hbonds/2'>hydrogen bonds</scene> (shown as dashed lines) from the <jmol>

<script>  select visible; spacefill 30%; delay 0.4; spacefill 40%; delay 0.4; spacefill 50%; delay 0.4; spacefill 100%; delay 0.8; spacefill 40%; delay 0.4; spacefill 20%; delay 0.4;

Apart from the characteristic hydrogen bonding patters, the other identifying feature of alpha helices are the main chain torsion angles <jmol>

</jmol>. If you plot phi against psi for each residue (so-called Ramachandran plot), you find that the phi/psi combination found in alpha helices fall into one of the three "allowed" (i.e. observed) areas for non-glycine residues. For a more detailed explanation with examples of Ramachandran plots, see [[Ramachandran Plot]] or [http://www.cryst.bbk.ac.uk/PPS95/course/3_geometry/rama.html Birkbeck's PPS95 course].

Proline is considered a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Here is an example of a <scene name='77/778341/Proline/1'>kink in a helix</scene> at the position of a <scene name='77/778341/Proline/2'>proline</scene>. Prolines are often found near the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). At the <scene name='77/778341/Proline_cap_detail/1'>C-terminal end</scene> of the helix, there is a proline that interrupts the regular pattern of n to n+4 hydrogen bonds.  Instead, the helix ends with an n to n+3 hydrogen bond (one turn of a so-called 3-10 helix, see [[Helices in Proteins]]). The subsequent proline is in the center of a turn, followed by a glycine (which is part of an n to n+3 hydrogen bond also typical for turns).

The first two protein structure to be determined, [[myoglobin]] and [[hemoglobin]], consists 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.

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 receptiors that illustrates this fold in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217).