Secondary structure - Revision history

Joel L. Sussman at 09:10, 31 January 2020

2020-01-31T09:10:18Z

←Older revision		Revision as of 09:10, 31 January 2020
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	* [[Membrane proteins]]		* [[Membrane proteins]]
	* [[Help:Color Keys]]		* [[Help:Color Keys]]
		+	* [[Basics of Protein Structure]]

	==External Resources==		==External Resources==
	* [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins where there is no empirically-determined 3D structure.		* [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins where there is no empirically-determined 3D structure.

Karsten Theis at 20:18, 20 July 2019

2019-07-20T20:18:19Z

←Older revision		Revision as of 20:18, 20 July 2019
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	There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.		There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.
-	*'''Helices'''. Alpha helix, pi helix and 3<sub>10</sub> helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</span> and <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> as shown in [[Helices in Proteins]].	+	*'''Helices'''. [[Alpha helix]], pi helix and 3<sub>10</sub> helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</span> and <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> as shown in [[Helices in Proteins]].

	*'''Strands'''. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel. These structural differences and other characteristics of β-sheets can be seen at [[Sheets in Proteins]].		*'''Strands'''. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel. These structural differences and other characteristics of β-sheets can be seen at [[Sheets in Proteins]].

Eric Martz: /* See Also */

2018-06-21T22:20:32Z

See Also

←Older revision		Revision as of 22:20, 21 June 2018
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	* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)		* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
	* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)		* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)
-	* [[Backbone representations]]	+	* [[Backbone representations]] explains backbone traces, smoothed traces, and ribbons ("cartoon" in JSmol).
	* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].		* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].
	* [[Calculate structure]]		* [[Calculate structure]]

Eric Martz: /* See Also */

2018-06-21T22:19:24Z

See Also

←Older revision		Revision as of 22:19, 21 June 2018
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	* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)		* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
	* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)		* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)
		+	* [[Backbone representations]]
	* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].		* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].
	* [[Calculate structure]]		* [[Calculate structure]]

Eric Martz: /* See Also */

2017-04-23T15:16:39Z

See Also

←Older revision		Revision as of 15:16, 23 April 2017
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	== See Also ==		== See Also ==
	* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)		* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
-	* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]]	+	* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)
	* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].		* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].
	* [[Calculate structure]]		* [[Calculate structure]]

Eric Martz: /* See Also */

2017-04-23T15:15:08Z

See Also

←Older revision		Revision as of 15:15, 23 April 2017
Line 73:		Line 73:
	== See Also ==		== See Also ==
	* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)		* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
		+	* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)\|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]]
	* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].		* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].
	* [[Calculate structure]]		* [[Calculate structure]]

Eric Martz: /* See Also */

2017-04-23T15:14:11Z

See Also

←Older revision

Revision as of 15:14, 23 April 2017

Wayne Decatur at 04:59, 22 November 2014

2014-11-22T04:59:39Z

←Older revision		Revision as of 04:59, 22 November 2014
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	<text>A progression from all atoms to cartoon</text>		<text>A progression from all atoms to cartoon</text>
	</jmolLink>		</jmolLink>
-	</jmol>illustrates the relationship of the protein backbone to the secondary structure representation. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.	+	</jmol> illustrates the relationship of the protein backbone to the secondary structure representation. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.

	==Displaying Secondary Structure==		==Displaying Secondary Structure==

Wayne Decatur at 04:58, 22 November 2014

2014-11-22T04:58:07Z

←Older revision		Revision as of 04:58, 22 November 2014
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	<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center><scene name='Secondary_structure/1dtg_ss/6'> Initial scene</scene> '''for Secondary Structures of Sample Proteins''' </center></td></tr></table>		<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center><scene name='Secondary_structure/1dtg_ss/6'> Initial scene</scene> '''for Secondary Structures of Sample Proteins''' </center></td></tr></table>
	{{Clear}}		{{Clear}}
-	The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helices</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helices</span>, <span style="color:yellow;background-color:black;font-weight:bold;">beta-sheets</span>, and <span style="color:#6080FF;background-color:white;font-weight:bold;">beta-turns</span>. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.	+	The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helices</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helices</span>, <span style="color:yellow;background-color:black;font-weight:bold;">beta-sheets</span>, and <span style="color:#6080FF;background-color:white;font-weight:bold;">beta-turns</span>. <jmol>
		+	<jmolLink>
		+	<script> load /wiki/scripts/60/609822/1dtg_ball_stick_label/1.spt;
		+	set echo top center;font echo 12 serif bolditalic;color echo white; echo "Start with all atoms of the protein\|as small spheres connected by sticks...";
		+	delay 4.0;
		+	echo "Next hide all but the backbone atoms\|keeping the connections shown...";
		+	select protein and sidechain;
		+	var a = [1,2,3,4,5,6,7,8]; for(var i IN a) {color translucent @i; delay 0.4;};
		+	delay 4.0;
		+	echo "The repeating patterns of the secondary structure\|elements are starting to be noticeable.";
		+	delay 3.0;
		+	select protein;
		+	echo "To help with observing the patterns,\|a tube tracing the backbone is revealed. ";
		+	var b = [0.01,0.05,0.1,0.2,0.3,0.4,0.45,0.5, 0.55]; for(var j IN b) {trace @j; delay 0.4;};
		+	echo "And fade out the spheres and stick backbone.. ";
		+	var c = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var k IN c) {spacefill @k; wireframe @k; delay 0.4;};
		+	wireframe off; spacefill off;
		+	echo "Finally fade in typical representation and\|coloring of the secondary structure. ";
		+	color cartoon structure;
		+	var d = [0.55,0.5,0.4,0.2, 0.1,0.05,0.01]; for(var m IN d) { var n = 0.56 - m;cartoon @n; color cartoon translucent @n; trace @m; delay 0.4;};
		+	trace off; delay 0.15; color cartoon translucent 0; cartoon on;
		+	</script>
		+	<text>A progression from all atoms to cartoon</text>
		+	</jmolLink>
		+	</jmol>illustrates the relationship of the protein backbone to the secondary structure representation. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.

	==Displaying Secondary Structure==		==Displaying Secondary Structure==

Wayne Decatur at 02:22, 21 November 2014

2014-11-21T02:22:20Z

←Older revision		Revision as of 02:22, 21 November 2014
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	*'''Turns'''. β-turn and γ-turn are the two types of turns. β-turns are composed of four amino acids and can have several difference conformations. γ-turns are made up of only three amino acids and are therefore a much tighter turn. More detail and illustrations of these turns are at [[Turns in Proteins]].		*'''Turns'''. β-turn and γ-turn are the two types of turns. β-turns are composed of four amino acids and can have several difference conformations. γ-turns are made up of only three amino acids and are therefore a much tighter turn. More detail and illustrations of these turns are at [[Turns in Proteins]].
-
-	The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helices</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helices</span>, <span style="color:yellow;background-color:black;font-weight:bold;">beta-sheets</span>, and <span style="color:#6080FF;background-color:white;font-weight:bold;">beta-turns</span>. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.
	{{Clear}}		{{Clear}}
	<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center><scene name='Secondary_structure/1dtg_ss/6'> Initial scene</scene> '''for Secondary Structures of Sample Proteins''' </center></td></tr></table>		<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center><scene name='Secondary_structure/1dtg_ss/6'> Initial scene</scene> '''for Secondary Structures of Sample Proteins''' </center></td></tr></table>
	{{Clear}}		{{Clear}}
		+	The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helices</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helices</span>, <span style="color:yellow;background-color:black;font-weight:bold;">beta-sheets</span>, and <span style="color:#6080FF;background-color:white;font-weight:bold;">beta-turns</span>. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> in addition to the above structures.
		+
	==Displaying Secondary Structure==		==Displaying Secondary Structure==
	If you want a convenient, static view of the structurally-determined [[Secondary structure\|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure''' will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right. The '''secondary structure''' will also be illustrated above the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].		If you want a convenient, static view of the structurally-determined [[Secondary structure\|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure''' will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right. The '''secondary structure''' will also be illustrated above the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].