User:Michael Roberts/Open-Day Demo: Difference between revisions

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==Representing protein structures==

'''Spacefill model'''

The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.

The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.

In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.

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'''Amino acid trace'''

Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>~~traces~~ the ~~chains~~</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!

Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!

One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.

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Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/2'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.

Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.

</StructureSection>

@@ Line 4: / Line 4: @@
-<StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'>
+<StructureSection load='1afq' size='600' side='right' caption=' ' scene='70/703491/Basic_representations/1'>
 ==Representing protein structures==
 '''Spacefill model'''
-The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called 'spacefill' view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.
+The view on the right shows a model of chymotrypsin, an enzyme that digests proteins in the gut. This is a so-called <scene name='70/703491/Basic_representations/1'>'spacefill'</scene> view, in which each atom is shown as a sphere. Different atoms are coloured individually: grey = carbon, red = oxygen, blue = nitrogen, ''etc''.
 In spacefill view, we can see the overall shape of the protein, but not much else. We cant see what's going on inside, for example.
@@ Line 22: / Line 22: @@
 '''Amino acid trace'''
-Here's a much more simplified view that <scene name='70/703491/Basic_representations/3'>traces the chains</scene> of amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
+Here's a much more simplified view that <scene name='70/703491/Basic_representations/4'>shows a trace of the backbone</scene> of the amino acids that make up the protein. Now we can see much more clearly the start and end of each chain (there are 3 chains in chymotrypsin, each coloured differently in this view), and how they are interwoven in the 3D structure. But this is now simplified too much to understand the details of the structure!
+One question this view does raise, is how the three separate chains are held together in the right way? The answer is the <scene name='70/703491/Basic_representations/5'>presence of disulphide bridges</scene> that link the chains together to form the correct overall structure.
@@ Line 63: / Line 65: @@
-Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/2'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.
+Finally, here's chymotrypsin with a molecule of <scene name='70/703491/Substrate/3'>substrate</scene> bound in its active site. Note how the substrate fits into a pocket on the surface of the enzyme.
 </StructureSection>