User:Michael Roberts/BIOL115 CaM - Revision history

Michael Roberts at 15:47, 13 April 2015

Michael Roberts — Mon, 13 Apr 2015 15:47:26 GMT

←Older revision		Revision as of 15:47, 13 April 2015
Line 50:		Line 50:
	== Binding to target proteins ==		== Binding to target proteins ==
	'''ACTIVE & 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 <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.	+	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.

Michael Roberts at 15:21, 13 April 2015

Michael Roberts — Mon, 13 Apr 2015 15:21:28 GMT

←Older revision		Revision as of 15:21, 13 April 2015
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	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].

Michael Roberts at 14:55, 13 April 2015

Michael Roberts — Mon, 13 Apr 2015 14:55:04 GMT

←Older revision		Revision as of 14:55, 13 April 2015
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	== 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.	+

Michael Roberts: Undo revision 2394006 by Michael Roberts (Talk)

Michael Roberts — Mon, 13 Apr 2015 11:36:54 GMT

Undo revision 2394006 by Michael Roberts (Talk)

←Older revision		Revision as of 11:36, 13 April 2015
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-	'''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.

Michael Roberts at 11:33, 13 April 2015

Michael Roberts — Mon, 13 Apr 2015 11:33:58 GMT

←Older revision		Revision as of 11:33, 13 April 2015
Line 21:		Line 21:


-	'''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'.	+	'''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'.
	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/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.	+	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.


	'''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/1'>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/5'>residues that take part in binding</scene> one of the Ca<sup>2+</sup> ions.

-	<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly.	+	<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/6'>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/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.	+	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.

Michael Roberts at 16:28, 3 May 2013

Michael Roberts — Fri, 03 May 2013 16:28:03 GMT

←Older revision		Revision as of 16:28, 3 May 2013
Line 56:		Line 56:

	'''CALMODULIN INTERACTS WITH ITS TARGET:'''		'''CALMODULIN INTERACTS WITH ITS TARGET:'''
-	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, ~~forcing it to adopt~~ an α-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.		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.

Michael Roberts at 16:17, 3 May 2013

Michael Roberts — Fri, 03 May 2013 16:17:37 GMT

←Older revision		Revision as of 16:17, 3 May 2013
Line 56:		Line 56:

	'''CALMODULIN INTERACTS WITH ITS TARGET:'''		'''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, forcing it to adopt 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.		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.

Michael Roberts at 16:35, 2 May 2013

Michael Roberts — Thu, 02 May 2013 16:35:57 GMT

←Older revision		Revision as of 16:35, 2 May 2013
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	'''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://~~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].

Michael Roberts at 16:28, 1 May 2013

Michael Roberts — Wed, 01 May 2013 16:28:51 GMT

←Older revision		Revision as of 16:28, 1 May 2013
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	Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.		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: ==		== 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.		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.

Michael Roberts at 16:27, 1 May 2013

Michael Roberts — Wed, 01 May 2013 16:27:09 GMT

←Older revision		Revision as of 16:27, 1 May 2013
Line 11:		Line 11:
	Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.		Click on the ''' 'green links' ''' in the text in the scrollable section below to examine this molecule in more detail.

-	<StructureSection load='1cll' size='~~600~~' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>	+	<StructureSection load='1cll' size='700' side='right' caption='Structure of human calmodulin (PDB entry [[1cll]])' scene='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>
	== Molecular Model: ==		== 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.		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.