Secondary structure: Difference between revisions

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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.

*'''Helices'''. Alpha helix, pi helix and 310 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 alpha helix, 310 helix and pi helix as shown in [[Helices in Proteins]].

*'''Helices'''. [[Alpha helix]], pi helix and 310 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 alpha helix, 310 helix and pi helix 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]].

*'''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 alpha helices, 310 helices, beta-sheets, and beta-turns. Another example, <scene name='Secondary_structure/Gly_phosphyl/3'>domain 2 of glycogen phosphorylase</scene> (PDB code [[1abb]]), contains a pi helix in addition to the above structures.

<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>~~'''Secondary Structures of Sample Proteins'''~~<scene name='Secondary_structure/1dtg_ss/6'> (Initial scene)</scene></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>

==~~Viewing~~ Secondary Structure==

The structure of a human transferrin n-lobe mutant (PDB code [[1dtg]]) shows the presence of alpha helices, 310 helices, beta-sheets, and beta-turns. <jmol>

~~Most~~ structures displayed in Proteopedia default to the cartoon view showing alpha helices and beta-sheets

If you need to see ~~them in~~ any Proteopedia structure window or any Jmol ~~window~~, ''click on the Jmol frank,'' and navigate the menu that comes up to first turn on the cartoons (''~~style~~''--->''~~scheme~~''--->''cartoon'') and then color this cartoon representation ~~as described above for added help~~ ( ''Color ~~cartoon~~'' ---> ''By Scheme'' -->''Secondary Structure'') .

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 pi helix in addition to the above structures.

==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 below the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].

Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any [[Jmol]] view, ''click on the Jmol frank,'' and navigate the menu that comes up to first first ''Select'' --> ''All'' and then turn on the cartoons (''Style''--->''Scheme''--->''cartoon'') and then for added help color this cartoon representation by the scheme outlined in the next section below ( ''Color''--> ''Structures'''--> ''Cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') . For advanced users, this is more easily accomplished by way of Jmol commands in the console, ''select all; cartoon on, color structure''.

Alternatively, use [[Scene authoring tools|Proteopedia's Scene Authoring Tools]] to display a structure as ''cartoon'' by selecting ''cartoon'' on the representation tab and then the ''color by structure'' button under the color tab.

If you want a convenient view of the structurally-determined '''secondary structure''' , as well as the '''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB code page and 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].

==How Jmol Determines Secondary Structure==

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== See Also ==

* [[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)

* [[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].

* [[Calculate structure]]

* [[Membrane proteins]]

* [[Help:Color Keys]]

* [[Basics of Protein Structure]]

==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.

Secondary structure: Difference between revisions

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@@ Line 4: / Line 4: @@
 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]].
 *'''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}}
-<table width='410' align='right' cellpadding='10'><tr><td bgcolor='#eeeeee'><center>'''Secondary Structures of Sample Proteins'''<scene name='Secondary_structure/1dtg_ss/6'> (Initial scene)</scene></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}}
-==Viewing Secondary Structure==
+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>
-Most structures displayed in Proteopedia default to the cartoon view showing alpha helices and beta-sheets
+ <jmolLink>
-If you need to see them in any Proteopedia structure window or any Jmol window, ''click on the Jmol frank,'' and navigate the menu that comes up to first turn on the cartoons (''style''--->''scheme''--->''cartoon'') and then color this cartoon representation as described above for added help ( ''Color cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') .
+  <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==
+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 below the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].
+Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any [[Jmol]] view, ''click on the Jmol frank,'' and navigate the menu that comes up to first first ''Select'' --> ''All'' and then turn on the cartoons (''Style''--->''Scheme''--->''cartoon'') and then for added help color this cartoon representation by the scheme outlined in the next section below ( ''Color''--> ''Structures'''--> ''Cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') . For advanced users, this is more easily accomplished by way of Jmol commands in the console, ''select all; cartoon on, color structure''.
 Alternatively, use [[Scene authoring tools|Proteopedia's Scene Authoring Tools]] to display a structure as ''cartoon'' by selecting ''cartoon'' on the representation tab and then the ''color by structure'' button under the color tab.
-If you want a convenient view of the structurally-determined '''secondary structure''' , as well as the '''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB code page and 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].
 ==How Jmol Determines Secondary Structure==
@@ Line 49: / Line 72: @@
 == See Also ==
+* [[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 presentaci&oacute;n)
+* [[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].
 * [[Calculate structure]]
 * [[Membrane proteins]]
 * [[Help:Color Keys]]
+* [[Basics of Protein Structure]]
 ==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.