Calmodulin: Difference between revisions

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[[Image:1prw.png|left|200px|thumb|Crystal structure of bovine brain Ca++ calmodulin in a compact form, [[1prw]]]]
<StructureSection load='1cll' size='350' side='right' scene='39/398280/Cv/3' caption='Human calmodulin complex with ethanol and Ca+2 ions (green) (PDB code [[1cll]])'>
{{STRUCTURE_1prw|  PDB=1prw  | SIZE=300| SCENE=Calmodulin/Cv/1 |right|CAPTION=Calmodulin, [[1prw]] }}
__TOC__
==Function==


Under contstruction...
[[Calmodulin]] (CaM) – calcium modulated protein – regulates various protein targets.  It is used by various proteins as calcium sensor and signal transducer by binding to their calcium binding domain (CBD).  It undergoes conformational change upon binding Ca++ via its 4 [[EF hand]] motives and can undergo post-translational modification. <scene name='39/398280/Cv/4'>Click here to see EF hand</scene> of Human calmodulin (PDB code [[1cll]]). <ref>PMID:1474585</ref> More details on apo-CaM [[Calcium-free Calmodulin]] and [[Calmodulin JMU]].
[[Calmodulin]] (CaM) – calcium modulated protein – regulates various protein targets.  It is used by various proteins as calcium sensor and signal transducer by binding to their calcium binding domain (CBD).  It undergoes conformational change upon binding Ca++ via its 4 EF hand motives and can undergo post-translational modification.
The images at the left and at the right correspond to one representative calmodulin, ''i.e.'' crystal structure of bovine brain Ca++ calmodulin in a compact form ([[1prw]]).
 
{{TOC limit|limit=2}}


{{Clear}}
{{Clear}}
<applet load='1cll' size='350' color='white' frame='true' align='right' caption='Calmodulin' scene='Calmodulin/Inicio/1' />


== [[Maximum Occurrence]] of Calmodulin Conformations ==


[http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520 Conformational change of Calmodulin]
[[Maximum Occurrence]], a method for making rigorous numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data, was used to probe the conformational disorder of Calmodulin<ref>doi:10.1021/ja1063923</ref>.<br />
[[Image:Movie_MOforproteopedia.gif|thumb|center|400px|Figure 3: Orientation tensor representation for 400 conformational states of Calmodulin, color coded according to their MO values (from less than 5% in blue to more than 30% in red).To better explain their meaning, 10 randomly chosen models are shown as cartoons and then replaced by the three axes of their color-coded orientation tensors.]] <br />
It was shown that the open ([[1cll]]) and closed ([[1prw]]) conformers can have MO of only 15% and 5% respectively.


[http://www.proteopedia.org/wiki/index.php/Calmodulin_in_motion 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]].


<scene name='Calmodulin/Inicio/1'>Unbound</scene>,
<jmol>
<scene name='Calmodulin/Bound/3'>Bound</scene>
<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>


== 3D Structures of Calmodulin ==
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 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>


=== Native CaM ===




[[1prw]], [[1deg]] – bCaM - bovine<br />
== 3D Structures of Calmodulin ==
[[1up5]] – cCaM – chicken<br />
[[Calmodulin 3D structures]]
[[1clm]], [[1osa]], [[1exr]] – PtCaM - ''Paramecium tetraurelia''<br />
[[3cln]] – rCaM - rat<br />
[[1x02]], [[1dmo]] – XlCaM – NMR - ''Xenopus laevis''<br />
[[2k61]], [[2k0e]] – hCaM – NMR - human<br />
[[1y6w]], [[1cll]] - hCaM<br />
[[4cln]] – DmCaM - ''Drosophila melanogaster''<br />
[[1rfj]] – CaM – potato<br />
[[1ooj]] – CaM – ''Caenorhabditis elegans''<br />
 
=== Mutant CaM ===
 
 
[[1ahr]] – cCaM (mutant)<br />
[[2k0j]], [[1sw8]] – hCaM (mutant) – NMR<br />
 
 
=== apo CaM ===
 
 
[[1lkj]] – yapoCaM – NMR -yeast<br />
[[1cfc]], [[1cfd]] - XlapoCaM – NMR<br />
[[1qx5]] – rapoCaM – rat<br />
 
 
=== CaM N-terminal ===
 
 
[[2i08]] - hCaM N-terminal (mutant)<br />
[[1j7o]] - hCaM N-terminal – NMR<br />
[[1f70]] - XlCaM N-terminal – NMR <br />
[[2ro8]], [[2roa]] - sCaM N-terminal+Ca – NMR - soybean<br />
[[2ro9]], [[2rob]] - sCaM C-terminal+Ca – NMR<br />
[[1j7o]], [[1j7p]] - hCaM N-terminal – NMR<br />
[[3ifk]], [[3b32]] – rCaM N-terminal <br />
[[1f54]], [[1f55]] – yapoCaM N-terminal – NMR<br />


 
</StructureSection>
=== CaM C-terminal ===
 
 
[[1f71]] - XlCaM C-terminal – NMR<br />
[[1cmg]] – bCaM C-terminal – NMR<br />
[[1fw4]] - bCaM C-terminal<br />
[[1cmf]] – bapoCaM C-terminal – NMR<br />
[[2hf5]] - hCaM EF2 EF3 – NMR<br />
 
 
=== CaM+ cations (not calcium) ===
 
 
[[2ksz]] – sCaM N-terminal+Mg – NMR <br />
[[1ak8]] - bCaM N-terminal+Ce – NMR<br />
[[2eqc]] – XlCaM C-terminal+Mg– NMR<br />
[[2pq3]] – rCaM+Zn<br />
[[2v01]] – hCaM+Pb<br />
[[2v02]] – hCaM+Ba<br />
[[1n0y]] – PtCaM+Pb <br />
 
 
=== CaM small molecule complexes ===
 
[[3if7]] – bCaM+sphingosylphosphorylcholine<br />
[[1qiv]], [[1qiw]] – bCaM+DPDv
[[1a29]], [[1lin]] – bCaM+trifluoperazine<br />
[[1ctr]] - hCaM+trifluoperazine <br />
[[2kug]], [[2kuh]] - hCaM N-terminal EF1 EF2+halothane – NMR<br />
[[2kdu]] – XlCaM+MUNC13-1 – NMR<br />
[[1mux]] – XlCaM+W-7 – NMR<br />
 
 
=== CaM complexed with protein CBD domains ===
 
 
[[3gp2]] – cCaM+CaM kinase II δ chain<br />
[[3gof]], [[2o60]] – cCaM+nitric oxide synthase  CBD<br />
[[1niw]] - rCaM+nitric oxide synthase  CBD <br />
[[3hr4]] - hCaM+nitric oxide synthase  CBD <br />
[[2x0g]], [[1yr5]], [[1wrz]] – hCaM+death-associated protein kinase 1 (DAP)<br />
[[2kne]] – hCaM+PMCA C-terminal CBD<br />
[[3ewt]], [[3ewv]] – hCaM+TNFR fragment<br />
[[2kn2]] – sCaM C-terminal+NtMKP1 CBD – NMR<br />
[[2w73]], [[2jzi]], [[2r28]] – hCaM+Ser/Thr phosphatase CBD<br />
[[3bya]] – hCaM+glutamate receptor peptide<br />
[[2hqw]] - rCaM+glutamate receptor peptide<br />
[[2k3s]] – CaM+smoothelin-like protein 1 – NMR<br />
[[3g43]], [[2vay]], [[2f3y]], [[2f3z]], [[2be6]] – hCaM+calcium channel CAV1.2<br />
[[3bxk]], [[3bxl]] – rCaM+ calcium channel peptide<br />
[[1cff]] - XlCaM+ calcium channel CBD - NMR<br />
[[1g4y]] - rCaM+ potassium channel CBD<br />
[[1qx7]] – rapoCaM+potassium channel peptide<br />
[[2o5g]] – cCaM+ myosin light chain kinase peptide<br />
[[2ix7]] – apoCaM+myosin-5A<br />
[[2k0f]] – hCaM+myosin light chain kinase peptide – NMR<br />
[[2bbm]], [[2bbn]] - DmCaM+myosin light chain kinase <br />
[[2bki]], [[2bkh]] – CaM+myosin VI – pig<br />
[[1zuz]] – hCaM+DRP kinase peptide<br />
[[2bcx]] – cCaM+ryanodine receptor 1 peptide<br />
[[2fot]] - bCaM+α-II spectrin CBD<br />
[[2f2o]], [[2f2p]] – bCaM+calcineurin CBD<br />
[[2col]], [[2yrt]], [[2yru]] – BpCaM+adenyl cyclase – ''Bordetella pertussis''<br />
[[1zot]] – BpCaM C-terminal+adenyl cyclase<br />
[[1xfu]], [[1xfv]], [[1xfw]], [[1xfx]], [[1xfy]], [[1xfz]], [[1y0v]], [[1sk6]], [[1pk0]], [[1lvc]], [[1k90]], [[1k93]] - CaM+adenyl cyclase – ''Bacillus anthracis''<br />
[[1sy9]] – XlCaM+olfactory channel peptide<br />
[[1xa5]] – bCaM+KAR-2<br />
[[1l7z]] – hCaM+CAP-23/NAP-22 CBD<br />
[[1qs7]], [[1qtx]] – CaM+RS20 – ''Escherichia coli''<br />
[[1vrk]] – CaM (mutant)+RS20<br />
[[1nwd]] – XlCaM+glutamate decarboxylase CBD<br />
[[1mxe]] – DmCaM+rCaMKI CBD <br />
[[1iq5]] – XlCaM+CaM dependent kinase CBD<br />
[[1cm1]], [[1cm4]], [[1cdm]] - bCaM+CaM dependent kinase CBD<br />
[[1cdl]] - hCaM+CaM dependent kinase CBD<br />
[[1ckk]] - XlCaM+CaM dependent kinase CBD - NMR<br />


==See Also==
==See Also==
Line 147: Line 177:
* [http://en.wikipedia.org/wiki/Calmodulin Calmodulin at Wikipedia]
* [http://en.wikipedia.org/wiki/Calmodulin Calmodulin at Wikipedia]
* [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb44_1.html Molecule of the Month (08/2003) at RCSB PDB]
* [http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb44_1.html Molecule of the Month (08/2003) at RCSB PDB]
*{{Proteopedia|2fot}} page for Calmodulin crystal complex between calmodulin and alpha11-[[spectrin]]
 
== Bibliography ==
<references/>
 
[[Category:Topic Page]]
Retrieved from "https://proteopedia.org/Calmodulin"