User:Michael Roberts/BIOL115 CaM: Difference between revisions

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[[Image:1cll.png|left|150px]]

'''Sequence and structure of EF hands'''

<span style="font-size:150%">'''Sequence and structure of EF hands'''</span>

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 ~~will~~ 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.

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.

'''MOLECULAR MODEL''':

~~Let~~'s start with a simple ~~<scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>~~ball-and-stick representation ~~</scene>~~of the protein. This shows all 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.

'''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 ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.

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 down 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 easily 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 in cartoon-style 'ribbons'.

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

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'''CALCIUM IONS''':

In each EF hand loop, the Ca2+ ions are bound by 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 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.

@@ Line 1: / Line 1: @@
 [[Image:1cll.png|left|150px]]
-'''Sequence and structure of EF hands'''
+<span style="font-size:150%">'''Sequence and structure of EF hands'''</span>
-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 will 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.
-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=''>
+<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''':
-Let's start with a simple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/3'>ball-and-stick representation </scene>of the protein. This shows all 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.
 '''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 ball-and-stick view shows us all the atoms, but if we're mainly interested in the overall structure of the protein, this can be too much detail.
-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 down 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 easily 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 in cartoon-style 'ribbons'.
 The alpha-helical region is now clearly defined, and there are also regions of beta-structure.
@@ Line 31: / Line 32: @@
 '''CALCIUM IONS''':
-In each EF hand loop, the Ca2+ ions are bound by 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 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.