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User:Michael Roberts/BIOL115 CaM: Difference between revisions

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<StructureSection load='1cll' size='600' side='right' caption='Structure of Human calmodulin (PDB entry [[1cll]])' scene=''>
<StructureSection load='1cll' size='600' side='right' caption='Structure of Human calmodulin (PDB entry [[1cll]])' scene=''>
Let's start with a simple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.
Let's start with a simple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.


'''BACKBONE''':
'''BACKBONE''':
The wireframe view shows us all the atoms, but this can be too much detail if we're mainly interested ion the overall structure of the protein.
The wireframe view shows us all the atoms, but this can be too much detail if we're mainly interested ion the overall structure of the protein.
This next veiw takes us right doewn to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now be seen.
This next veiw takes us right doewn to a minimal representation that simply traces the <scene name='User:Michael_Roberts/BIOL115_CaM/Backbone/1'>"backbone" </scene>of the protein. The backbone includes the peptide linkages between each amino acid, along with the alpha-carbon atoms to which the side chains are attached. Notice that helical regions can now be seen.


'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them as ribbons.  
'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/2'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them as ribbons.  
The alpha-helical region is now clearly defined, and there are also regions of beta-structure.
The alpha-helical region is now clearly defined, and there are also regions of beta-structure.
Colour key:
Colour key:
{{Template:ColorKey_Helix}},
{{Template:ColorKey_Helix}},
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The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.
The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.


'''CALCIUM IONS''':
'''CALCIUM IONS''':
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The structure shown has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>Ca2+ ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.
The structure shown has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>Ca2+ ions</scene> bound. In this condition, the protein adopts the extended structure shown. The EF hand-forming helices are bent away from the long linking helix, revealing hydrophobic residues and exposing the linking chain.


'''CO-ORDINATING RESIDUES''':
'''CO-ORDINATING RESIDUES''':
To illustrate how Ca2+  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.
To illustrate how Ca2+  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.
<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>'''ZOOM'''</scene> to see this more clearly.  
<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly.  
 


'''CO-ORDINATING ATOMS''':
'''CO-ORDINATING ATOMS''':
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'''INACTIVE CALMODULIN:'''
At resting levels of  cytosolic Ca2+ (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called apo-calmodulin and <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>its structure </scene>is more compact.
The terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not a helical along its whole length, is not exposed.
'''CALMODULIN INTERACTS WITH ITS TARGET:'''
The Ca2+-bound form of calmodulin with its exposed hydrophobic surfaces that you have already observed can <scene name='User:Michael_Roberts/BIOL115_CaM/Active_calmodulin/1'>interact with a target protein</scene>. It does this by wrapping around a specific sequence on the target molecule, forcing it to adopt an a-helical structure.
The target molecule here is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.


End of section
End of section
</StructureSection>
</StructureSection>
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