Alpha helix - Revision history

Eric Martz: /* See Also */

Eric Martz — Sun, 09 Jul 2023 17:08:07 GMT

Karsten Theis: /* Alpha helices in transmembrane proteins */

Karsten Theis — Sat, 08 Jul 2023 22:26:32 GMT

Alpha helices in transmembrane proteins

←Older revision		Revision as of 22:26, 8 July 2023
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	===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 ~~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===		===Alpha helices in coiled coils===

Karsten Theis: /* Alpha helices in soluble (globular) proteins */

Karsten Theis — Sat, 08 Jul 2023 22:07:57 GMT

Alpha helices in soluble (globular) proteins

←Older revision		Revision as of 22:07, 8 July 2023
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	==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 ~~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===		===Alpha helices in transmembrane proteins===

Karsten Theis at 09:56, 7 August 2021

Karsten Theis — Sat, 07 Aug 2021 09:56:47 GMT

←Older revision		Revision as of 09:56, 7 August 2021
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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 strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.	+	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==

Karsten Theis at 08:27, 7 August 2021

Karsten Theis — Sat, 07 Aug 2021 08:27:33 GMT

←Older revision		Revision as of 08:27, 7 August 2021
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-	==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.		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.

		+	==Structure, hydrogen bonding and composition==
		+	<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;

Karsten Theis: Undo revision 3288155 by Karsten Theis (Talk)

Karsten Theis — Wed, 02 Sep 2020 21:46:08 GMT

Undo revision 3288155 by Karsten Theis (Talk)

←Older revision		Revision as of 21:46, 2 September 2020
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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 strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.		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 ~~<scene name='77/778341/Testing/1'>~~main chain~~</scene>~~ 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>

Karsten Theis at 21:44, 2 September 2020

Karsten Theis — Wed, 02 Sep 2020 21:44:59 GMT

←Older revision		Revision as of 21:44, 2 September 2020
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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 strand), i.e. all residues have similar conformation and hydrogen bonding, and it can be of arbitrary length.		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>	+	In an alpha helix, the <scene name='77/778341/Testing/1'>main chain</scene> 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>

Eric Martz: /* Quiz */

Eric Martz — Fri, 01 Feb 2019 13:08:17 GMT

Quiz

←Older revision		Revision as of 13:08, 1 February 2019
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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. ~~PRimary~~ structure	+	-A. Primary structure
	+B. Secondary structure		+B. Secondary structure
	-C. Tertiary structure		-C. Tertiary structure
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	</quiz>		</quiz>
-

	==See Also==		==See Also==

Eric Martz: /* See Also */

Eric Martz — Sat, 19 May 2018 23:19:41 GMT

Eric Martz: /* See Also */

Eric Martz — Sat, 19 May 2018 23:17:59 GMT

←Older revision		Revision as of 17:08, 9 July 2023
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	* [[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]]		* [[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]]

←Older revision		Revision as of 23:19, 19 May 2018
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	* [[Helices in Proteins]]: alpha, 3<sub>10</sub>, and pi helices side by side.		* [[Helices in Proteins]]: alpha, 3<sub>10</sub>, and pi helices side by side.
	* [[Proteins: primary and secondary structure]]		* [[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]]		* [[Protein primary, secondary, tertiary and quaternary structure]] / [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]]

←Older revision		Revision as of 23:17, 19 May 2018
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	==See Also==		==See Also==
	* [[Helices in Proteins]]: alpha, 3<sub>10</sub>, and pi helices side by side.		* [[Helices in Proteins]]: alpha, 3<sub>10</sub>, and pi helices side by side.
		+	* [[Proteins: primary and 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]]

	== References ==		== References ==
	<references/>		<references/>
	[[Category:Pages with quizzes]]		[[Category:Pages with quizzes]]