Secondary structure: Difference between revisions

Line 12:

<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>

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.

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>

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==

Secondary structure: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 12: / Line 12: @@
 <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}}
-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==