Calmodulin: Difference between revisions

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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 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;
delete protein and not alpha;
delete protein and not backbone;
select all;cartoon only;cartoon off;
select all;cartoon only;cartoon off;
select 4-147;cartoon on;
select 4-147;cartoon on;
Line 39: 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}, {(4-78) 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 55: 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, {8-78}, {79}, {(4-78) 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 64: Line 66:
</jmol>
</jmol>


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>


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 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>
<!-- <center><swf width="720" height="576">/flash/Apo_CaM_CaCaM.swf</swf></center> -->
<jmolButton>
 
<script>
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.
script "/wiki/images/a/a2/Storymorph.spt";
 
load files "=1prw" "=1cll";
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).
delete water;
 
delete protein and not backbone;
This movie was created by Andrei, Zini et al., of the
select all;cartoon only;cartoon off;
[http://www.scivis.ifc.cnr.it Scientific Visualization Unit],  
select 4-147;cartoon on;
Institute of Clinical Physiology - CNR  of Itlay.
model 1;
 
center visible;color group;
[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520 Conformational change of Calmodulin]
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>


<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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