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==

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 strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.

In an alpha helix, the main chain arranges in a <scene name='77/778341/Ribbon/1'>right-handed helix</scene> with the <jmol><jmolLink>

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<text>side chains</text>

</jmolLink></jmol> pointing away from the helical axis. (Stereo: <jmol><jmolLink>

<script> stereo 5

<script> stereo -5

</script>

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</jmol>) at the position of a <scene name='77/778341/Proline/5'>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).

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/5'>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.

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==Types of proteins and folds that contain alpha helices==

===Alpha helices in soluble (globular) proteins===

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.

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===

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).

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===

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* [[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 ==

[[Category:Pages with quizzes]]

Alpha helix: Difference between revisions

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@@ Line 1: / Line 1: @@
+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==
 <StructureSection load='1hhb' size='400' side='right' caption='alpha helix' scene='77/778341/Ballstick/1'>
-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 strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.
 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;
@@ Line 8: / Line 8: @@
    <text>side chains</text>
 </jmolLink></jmol> pointing away from the helical axis. (Stereo: <jmol><jmolLink>
-<script>  stereo 5
+<script>  stereo -5
    </script>
    <text>ON</text>
@@ Line 54: / Line 54: @@
 </jmol>) at the position of a <scene name='77/778341/Proline/5'>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).
+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/5'>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.
@@ Line 64: / Line 64: @@
 ==Types of proteins and folds that contain alpha helices==
 ===Alpha helices in soluble (globular) proteins===
-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.
+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===
-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).
+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===
@@ Line 126: / Line 126: @@
 * [[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/>
 [[Category:Pages with quizzes]]