Calmodulin: Difference between revisions

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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
 
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== Calmodulin in Motion ==
== Calmodulin in Motion ==


The buttons below allow you to explore a morph between structures [[1prw]] and [[1cll]].  
The buttons below allow you to explore morphs <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] creates the interpolated coordinates of the morph on the fly.</ref> between structures [[1prw]] and [[1cll]].
 
<jmol>
<jmol>
<jmolButton>
<jmolButton>
<script>
<script>
script "/wiki/images/1/1a/Morph.spt";
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
load files "=1prw" "=1cll";
delete water;
delete water;
Line 40: Line 41:
structures = [{1.1}, {2.1}];
structures = [{1.1}, {2.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {79-147},{79-147}, {(79-138) and alpha}, 0],  
[{79-147},{79-147}, {(79-138) and alpha}],  
[0, 1, 0, {4-78}, {79}, {(8-78) and alpha}, 0],
[{4-78}, {79}, {(8-78) and alpha}],
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Open</text>
<text>Open</text>
Line 56: Line 57:
structures = [{2.1}, {1.1}];
structures = [{2.1}, {1.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {79-147},{79-147}, {(79-138) and alpha}, 0],  
[{79-147},{79-147}, {(79-138) and alpha}],  
[0, 1, 0, {4-78}, {79}, {(8-78) and alpha}, 0],
[{4-78}, {79}, {(8-78) and alpha}],
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Close</text>
<text>Close</text>
Line 69: Line 70:
<jmolButton>
<jmolButton>
<script>
<script>
script "/wiki/images/1/1a/Morph.spt";
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
load files "=1prw" "=1cll";
delete water;
delete water;
Line 90: Line 91:
structures = [{1.1}, {2.1}];
structures = [{1.1}, {2.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {79-147},{79-147}, {(79-138) and alpha}, 0],  
[{79-147},{79-147}, {(79-138) and alpha}],  
[0, 1, 0, {4-78}, {79}, {(8-78) and alpha}, 0],
[{4-78}, {79}, {(8-78) and alpha}],
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Open</text>
<text>Open</text>
Line 106: Line 107:
structures = [{2.1}, {1.1}];
structures = [{2.1}, {1.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {79-147},{79-147}, {(79-138) and alpha}, 0],  
[{79-147},{79-147}, {(79-138) and alpha}],  
[0, 1, 0, {4-78}, {79}, {(8-78) and alpha}, 0],
[{4-78}, {79}, {(8-78) and alpha}],
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Close</text>
<text>Close</text>
Line 119: Line 120:
<jmolButton>
<jmolButton>
<script>
<script>
script "/wiki/images/1/1a/Morph.spt";
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
load files "=1prw" "=1cll";
delete water;
delete water;
Line 140: Line 141:
structures = [{1.1}, {2.1}];
structures = [{1.1}, {2.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {4-78}, {4-78}, {(8-78) and alpha}, 0],
[{4-78}, {4-78}, {(8-78) and alpha}],
[0, 1, 0, {79-147},{78}, {(79-138) and alpha}, 0],  
[{79-147},{78}, {(79-138) and alpha}],  
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Open</text>
<text>Open</text>
Line 156: Line 157:
structures = [{2.1}, {1.1}];
structures = [{2.1}, {1.1}];
my_recipe = [  
my_recipe = [  
[0, 1, 0, {4-78}, {4-78}, {(8-78) and alpha}, 0],
[{4-78}, {4-78}, {(8-78) and alpha}],
[0, 1, 0, {79-147},{78}, {(79-138) and alpha}, 0],  
[{79-147},{78}, {(79-138) and alpha}],  
];
];
morph(20, structures, my_recipe, 0);
morph(20, structures, my_recipe);
</script>
</script>
<text>Close</text>
<text>Close</text>
Line 165: Line 166:
</jmol>
</jmol>


The clip represents Calmodulin in motion. At the beginning it is shown moving in the unbound form (ApoCaM), and it changes its conformation when Calcium ions are present in the medium (CaCaM).
<!-- <center><swf width="720" height="576">/flash/Apo_CaM_CaCaM.swf</swf></center> -->
Motion of ApoCaM is elaborated on the basis of 23 conformations derived from NMR file [[1cfc]], using the 3D animation program Blender, and according to a system to be published soon (Zini et al., manuscript in preparation). The transition from ApoCaM to CaCaM is elaborated with Blender starting with conformation 21 of 1cfc to arrive in conformation 11 of pdb file 1x02.
Surface rendering is also elaborated using Blender, and shows the lipophilic potential as a scale of white-black and smooth-rough, form the most lipophilic to the hydrophilic. Electrostatic potential is represented as a series of lines moving in the direction Positive to Negative, elaborated according to a scheme to be published soon (Andrei et al., in preparation). As most lines are moving towards Calmodulin, one can learn that the protein is slightly acidic (negative partial charges on its surface).
This movie was created by Andrei, Zini et al., of the
[http://www.scivis.ifc.cnr.it Scientific Visualization Unit],
Institute of Clinical Physiology - CNR  of Itlay.
[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520 Conformational change of Calmodulin]
<scene name='Calmodulin/Inicio/1'>Unbound</scene>,
<scene name='Calmodulin/Bound/4'>Bound</scene>


{{Clear}}


== 3D Structures of Calmodulin ==
== 3D Structures of Calmodulin ==

Latest revision as of 19:03, 7 July 2023

Human calmodulin complex with ethanol and Ca+2 ions (green) (PDB code 1cll)

Drag the structure with the mouse to rotate

See Also

Bibliography

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