User:Michael Roberts/BIOL115 CaM: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
mNo edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 21: Line 21:




'''SECONDARY STRUCTURE''': This is shown more clearly by a <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/5'>ribbon diagram</scene>. The computer calculates where regions of secondary structure occur and draws them in cartoon-style '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 in cartoon-style 'ribbons'.  
The α-helical region is now clearly defined, and there are also regions of β-structure.
The α-helical region is now clearly defined, and there are also regions of β-structure.


Line 35: Line 35:
In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.
In each EF hand loop, the Ca<sup>2+</sup> ions are bound by amino acid residues in and near the loops.


The structure shown here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/4'>calcium 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 here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>calcium 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 Ca<sup>2+</sup>  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/5'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.
To illustrate how Ca<sup>2+</sup>  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.


<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/6'>Zoom in</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''':
To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/4'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.  
To highlight the atoms that co-ordinate the Ca<sup>2+</sup> ion, we can now enlarge those that are close (within 2.7 Å). This shows that <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/3'>seven oxygen</scene> atoms form the calcium co-ordination shell. Five are contributed by the side chain carboxyl groups of Asp and Glu and a sixth by the peptide carbonyl of Gln. The seventh oxygen is provided by an associated water molecule.  




== Binding to target proteins ==
== Binding to target proteins ==
'''INACTIVE CALMODULIN:'''
'''ACTIVE & INACTIVE CALMODULIN:'''
At resting levels of  cytosolic Ca<sup>2+</sup> (~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.
At resting levels of  cytosolic Ca<sup>2+</sup> (~100 nM), calmodulin exists predominantly in the calcium-free form. This is called <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>apo-calmodulin</scene> and its structure is more compact than the structure we saw earlier <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'>with bound calcium</scene>. Note the extended α-helix linking the two EF-hand-containing domains in the Ca-bound structure, which is interrupted in the <scene name='User:Michael_Roberts/BIOL115_CaM/Inactive_calmodulin/1'>Ca-free form</scene>. Here, the terminal helices are folded down concealing their hydrophobic surfaces and the central chain, which is not now α-helical along its whole length, is not exposed.
 
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.




Line 59: Line 57:


The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.
The target molecule here (shown in blue) is the calmodulin-regulated enzyme, myosin light chain kinase. Only a short sequence from this protein, the calmodulin binding domain, is shown.
In this view, <scene name='54/541097/Active_calmodulin/3'>polar and non-polar residues</scene> are coloured in order to highlight the hydrophobic interior of the molecule, which forms the binding site for the myosin light chain kinase calmodulin binding domain.
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
</StructureSection>
</StructureSection>


'''External Resources.'''
'''External Resources.'''
You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].
You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://morph2.molmovdb.org/results.rpy?jobid=8350057535].
Retrieved from "https://proteopedia.org/User:Michael_Roberts/BIOL115_CaM"