User:Michael Roberts/BIOL115 CaM: Difference between revisions

(8 intermediate revisions by the same user not shown)

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Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.

== Molecular Model: ==

We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.

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== Binding to target proteins ==

'''INACTIVE CALMODULIN:'''

'''ACTIVE & 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~~.

At resting levels of cytosolic Ca2+ (~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.

'''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 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, which is then forced into an α-helical structure.

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>

'''External Resources.'''

You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://~~www~~.molmovdb.org/~~cgi-bin/morph~~.~~cgi~~?ID=~~b097743-28520~~].

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].

@@ Line 11: / Line 11: @@
 Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.
-<StructureSection load='1cll' size='700' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>
+<StructureSection load='1cll' size='600' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>
 == Molecular Model: ==
 We'll start with a simple ball-and-stick representation of the protein. This shows all of the atoms that make up the protein and the bonds between them.
@@ Line 49: / Line 49: @@
 == 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.
 '''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 Ca<sup>2+</sup>-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, which is then forced into an α-helical structure.
 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>
 '''External Resources.'''
-You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [http://www.molmovdb.org/cgi-bin/morph.cgi?ID=b097743-28520].
+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].