User:Michael Roberts/BIOL115 CaM: Difference between revisions

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The EF hand motif is present in a many proteins and it commonly bestows the ability to bind ~~Ca2~~+ ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the ~~Ca2~~+-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca2+-binding proteins.

The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca2+ ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca2+-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca2+-binding proteins.

The structure below, obtained by X-ray crystallography, represents the Ca2+-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three a helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.

The structure below, obtained by X-ray crystallography, represents the Ca2+-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.

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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'''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 ~~alpha~~-helical region is now clearly defined, and there are also regions of ~~beta~~-structure.

The α-helical region is now clearly defined, and there are also regions of β-structure.

Colour key:

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'''CALCIUM IONS''':

In each EF hand loop, the Ca2+ ions are bound by amino acid residues in and near the loops.

In each EF hand loop, the Ca2+ 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'>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 here 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''':

To illustrate how Ca2+ 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 Ca2+ ions.

To illustrate how Ca2+ 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 Ca2+ ions.

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

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'''CO-ORDINATING ATOMS''':

To highlight the atoms that co-ordinate the Ca2+ 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 Ca2+ 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.

'''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 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.

@@ Line 4: / Line 4: @@
-The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca2+ ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca2+-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular Ca2+-binding proteins.
+The EF hand motif is present in a many proteins and it commonly bestows the ability to bind Ca<sup>2+</sup> ions. It was first identified in parvalbumin, a muscle protein. Here we'll have a look at the Ca<sup>2+</sup>-binding protein [[calmodulin]], which possesses four EF hands. Calmodulin and its isoform, troponinC, are important intracellular <sup>Ca2+</sup>-binding proteins.
-The structure below, obtained by X-ray crystallography, represents the Ca2+-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three a helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.
+The structure below, obtained by X-ray crystallography, represents the <sup>Ca2+</sup>-binding protein calmodulin. It has a dumbell-shaped structure with two identical lobes connected by a central alpha-helix. Each lobe comprises three α-helices joined by loops. A helix-loop-helix motif forms the basis of each EF hand.
 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='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 22: / Line 22: @@
 '''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 alpha-helical region is now clearly defined, and there are also regions of beta-structure.
+The α-helical region is now clearly defined, and there are also regions of β-structure.
 Colour key:
@@ Line 32: / Line 32: @@
 '''CALCIUM IONS''':
-In each EF hand loop, the Ca2+ ions are bound by amino acid residues in and near the loops.
+In each EF hand loop, the <sup>Ca2+</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'>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 here has four <scene name='User:Michael_Roberts/BIOL115_CaM/Structure_plus_c/3'><sup>Ca2+</sup> 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''':
-To illustrate how Ca2+  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 Ca2+ ions.
+To illustrate how <sup>Ca2+</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 <sup>Ca2+</sup> ions.
 <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>Zoom in</scene> to see this more clearly.
@@ Line 44: / Line 44: @@
 '''CO-ORDINATING ATOMS''':
-To highlight the atoms that co-ordinate the Ca2+ 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 <sup>Ca2+</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.
 '''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 <sup>Ca2+</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.
 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.