User:Michael Roberts/BIOL115 CaM: Difference between revisions

Line 11:

Let's start with a ~~sinmple~~ <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.

Let's start with a simple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.

'''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. 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 a-carbon atoms to which ~~R-groups~~ are attached. Notice that helical regions can now be seen.

'''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.

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.

'''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.

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

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

{{Template:ColorKey_Helix}},

{{Template:ColorKey_Strand}},

{{Template:ColorKey_Turn}}.

The short anti-parallel b-sheet between the adjacent EF hand loops are observed in calmodulins from various species.

The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.

'''CALCIUM IONS''': In each EF hand loop, the Ca2+ ions are bound by residues in and near the loops.

'''CALCIUM IONS''':

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

'''CO-ORDINATING RESIDUES''': To illustrate how Ca2+ is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.

'''CO-ORDINATING RESIDUES''':

To illustrate how Ca2+ is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.

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

'''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 seven oxygen 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.

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

End of section

</StructureSection>

@@ Line 11: / Line 11: @@
 <StructureSection load='1cll' size='600' side='right' caption='Structure of Human calmodulin (PDB entry [[1cll]])' scene=''>
-Let's start with a sinmple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.
+Let's start with a simple <scene name='User:Michael_Roberts/BIOL115_CaM/Wireframe/2'>wireframe representation </scene>of the protein. This shows all the bonds between the atoms that make up the protein.
-'''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. 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 a-carbon atoms to which R-groups are attached. Notice that helical regions can now be seen.
+'''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.
+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.
 '''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.
-The a-helical region is now clearly defined, and there are also regions of b-structure.
+The alpha-helical region is now clearly defined, and there are also regions of beta-structure.
 {{Template:ColorKey_Helix}},
 {{Template:ColorKey_Strand}},
 {{Template:ColorKey_Turn}}.
-The short anti-parallel b-sheet between the adjacent EF hand loops are observed in calmodulins from various species.
+The short anti-parallel beta-sheet between the adjacent EF hand loops are observed in calmodulins from various species.
-'''CALCIUM IONS''': In each EF hand loop, the Ca2+ ions are bound by residues in and near the loops.
+'''CALCIUM IONS''':
+In each EF hand loop, the Ca2+ ions are bound by 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.
-'''CO-ORDINATING RESIDUES''': To illustrate how Ca2+  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.
+'''CO-ORDINATING RESIDUES''':
+To illustrate how Ca2+  is bound, this display shows the <scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/1'>residues </scene>that take part in binding one of the Ca2+ ions.
+<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>'''ZOOM'''</scene> to see this more clearly.
+'''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 seven oxygen 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.
-<scene name='User:Michael_Roberts/BIOL115_CaM/Co-ordination/2'>'''ZOOM'''</scene> to see this more clearly.
 End of section
 </StructureSection>