User:Michael Roberts/BIOL115 CaM
From Proteopedia
(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 | + | 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 | + | 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. | 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 | + | <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. | ||
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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'. | '''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 | + | The α-helical region is now clearly defined, and there are also regions of β-structure. |
Colour key: | Colour key: | ||
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'''CALCIUM IONS''': | '''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''': | '''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. | <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''': | '''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:''' | '''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. | 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. | ||
Revision as of 15:14, 12 April 2013
Sequence and structure of EF hands
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 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.
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External Resources. You can view a nice animation of the conformational change undergone by calmodulin upon calcium binding by following this link [1].
