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

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==Interactive visualisation of 3D protein structures==

~~<StructureSection load='1afq' size='600' side='right' caption='Structure~~ of ~~bovine chymotrypsin~~ (~~PDB entry [[1afq]]~~)' ~~scene='70/703491/Basic_representations/1'>~~

Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.

== Spacefill view ==

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''.

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.

~~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.~~

== Ball-and-stick molecular model ==

This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.

Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example.

== 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!

What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.

</StructureSection>

~~== References ==~~

~~<references/>~~

@@ Line 1: / Line 1: @@
 ==Interactive visualisation of 3D protein structures==
-<StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'>
+Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.
-Understanding the 3-dimensional structures of proteins is key to understanding their functions. Identifying the positions of all the different atoms that make up an individual protein (there are usually several thousand atoms in a single protein) is a big job, but once achieved, we can use a range of tools to visualise protein structures. Here, we'll have a look at some different ways of representing molecular structures of proteins, and in so doing, start to see the key structural elements that characterise protein structure.
+<StructureSection load='1afq' size='600' side='right' caption='Structure of bovine chymotrypsin (PDB entry [[1afq]])' scene='70/703491/Basic_representations/1'>
+== Spacefill view ==
 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''.
+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.
-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.
+== Ball-and-stick molecular model ==
 This view shows chymotrypsin in the familiar <scene name='70/703491/Basic_representations/2'>'ball and stick'</scene> representation. Atoms are indicated by small spheres, with the sticks that link them together representing covalent bonds.
+Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example.
-Now we can see all the atoms in the protein, but again, it's difficult to get a feel for how it is organised. It's very difficult to follow the chain of amino acids that makes up the protein, for example.
+== 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!
 What we really need to do next is to have a basic [http://www.proteopedia.org/wiki/index.php/Introduction_to_Protein_Structure introduction to protein structure]. This link will take you to a page that introduces you to the basic concepts.
 </StructureSection>
-== References ==
-<references/>