Alpha helix: Difference between revisions
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m kinked helix with two rockets (had to manually set secondary structure to turn at site of kink) |
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Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to [https://en.wikipedia.org/wiki/List_of_protein_secondary_structure_prediction_programs predict] where helices occur in a protein sequence. | Some amino acids are commonly found in alpha helices and others are rare. Amino acids with a side chain whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, i.e. occur less often in alpha helices than in other secondary structure elements. Glycine, with its many possible main chain conformations, is also rarely found in helices. Knowing how likely an amino acid is to occur in an alpha helix (the so-called helix propensities), it is possible to [https://en.wikipedia.org/wiki/List_of_protein_secondary_structure_prediction_programs predict] where helices occur in a protein sequence. | ||
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/3'>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/2'>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). | 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/3'>kink in a helix</scene> (<jmol> | ||
<jmolLink> | |||
<script> select 58-61:A; structure turn; | |||
</script> | |||
<text>fit rockets...</text> | |||
</jmolLink> | |||
</jmol> ) 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/2'>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 beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812/ sequence and structural patterns] involving main chain or side chain hydrogen bonding. | The beginnings and ends of helices are called N-caps and C-caps, respectively, and they have interesting [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812/ sequence and structural patterns] involving main chain or side chain hydrogen bonding. | ||