Calmodulin: Difference between revisions

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== Calmodulin in Motion ==
== Calmodulin in Motion ==


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).
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]].


<!-- <center><swf width="720" height="576">/flash/Apo_CaM_CaCaM.swf</swf></center> -->
<jmol>
<jmolButton>
<script>
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
delete water;
delete protein and not backbone;
select all;cartoon only;cartoon off;
select 4-147;cartoon on;
model 1;
center visible;color group;
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{4-138}{4-138} ROTATE TRANSLATE;
</script>
<text>Prepare Animation</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 2;
display 4-147;
backbone only;
backbone 0.5
structures = [{1.1}, {2.1}];
my_recipe = [
[{79-147},{79-147}, {(79-138) and alpha}],
[{4-78}, {79}, {(8-78) and alpha}],
];
morph(20, structures, my_recipe);
</script>
<text>Open</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 1
display 4-147;
backbone only;
backbone 0.5
structures = [{2.1}, {1.1}];
my_recipe = [
[{79-147},{79-147}, {(79-138) and alpha}],
[{4-78}, {79}, {(8-78) and alpha}],
];
morph(20, structures, my_recipe);
</script>
<text>Close</text>
</jmolButton>
</jmol>


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.
The following morph is between [[1prw]] and [[1cll]] after superposition of residues 79-138. This shows the subtle conformational changes in that domain more clearly.
<jmol>
<jmolButton>
<script>
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
delete water;
delete protein and not backbone;
select all;cartoon only;cartoon off;
select 4-147;cartoon on;
model 1;
center visible;color group;
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{79-138}{79-138} ROTATE TRANSLATE;
</script>
<text>Prepare Animation</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 2;
display 4-147;
backbone only;
backbone 0.5
structures = [{1.1}, {2.1}];
my_recipe = [
[{79-147},{79-147}, {(79-138) and alpha}],
[{4-78}, {79}, {(8-78) and alpha}],
];
morph(20, structures, my_recipe);
</script>
<text>Open</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 1
display 4-147;
backbone only;
backbone 0.5
structures = [{2.1}, {1.1}];
my_recipe = [
[{79-147},{79-147}, {(79-138) and alpha}],
[{4-78}, {79}, {(8-78) and alpha}],
];
morph(20, structures, my_recipe);
</script>
<text>Close</text>
</jmolButton>
</jmol>


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).
The following morph is between [[1prw]] and [[1cll]] after superposition of residues 8-78. This shows the subtle conformational changes in that domain more clearly.
<jmol>
<jmolButton>
<script>
script "/wiki/images/a/a2/Storymorph.spt";
load files "=1prw" "=1cll";
delete water;
delete protein and not backbone;
select all;cartoon only;cartoon off;
select 4-147;cartoon on;
model 1;
center visible;color group;
compare {2.1} {1.1} SUBSET{*.CA} ATOMS{8-78}{8-78} ROTATE TRANSLATE;
</script>
<text>Prepare Animation</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 2;
display 4-147;
backbone only;
backbone 0.5
structures = [{1.1}, {2.1}];
my_recipe = [
[{4-78}, {4-78}, {(8-78) and alpha}],
[{79-147},{78}, {(79-138) and alpha}],
];
morph(20, structures, my_recipe);
</script>
<text>Open</text>
</jmolButton>
</jmol><jmol>
<jmolButton>
<script>
model 1
display 4-147;
backbone only;
backbone 0.5
structures = [{2.1}, {1.1}];
my_recipe = [
[{4-78}, {4-78}, {(8-78) and alpha}],
[{79-147},{78}, {(79-138) and alpha}],  
];
morph(20, structures, my_recipe);
</script>
<text>Close</text>
</jmolButton>
</jmol>


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 ==
Retrieved from "https://proteopedia.org/Calmodulin"