User:J. Shaun Lott/BIOSCI 203: Difference between revisions

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BIOSCI 203 Lab 2 - Protein structure

== '''BIOSCI 203 Lab 2 - Protein structure''' ==

----

~~You are viewing~~ a protein structure using the Jmol viewer within Proteopedia. Jmol is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll bar to zoom in and out, and the right mouse button for more options and information.

On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within Proteopedia. Jmol is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll bar to zoom in and out, and the right mouse button for more options and information. Try this out for yourself now ==>

The protein we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme hORF6. Click

<scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfer atoms. Pretty hard to look at, isn't it?

We can simplify things by just showing a cartoon that traces the path of the amino acid backbone - α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/2'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/1'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.

~~We will be looking at~~ the structure ~~of the N-terminal domain of the human 1-Cys peroxidase enzyme~~

It can help to see the

<scene name='User:J._Shaun_Lott/BIOSCI_203/~~All_atoms_view~~/1'>~~hORF6~~</scene>.

<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/1'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>C-α trace</scene> rather than a ribbon diagram.

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 <applet load="HORF6.pdb" size="500" color="white" frame="true" align="right" caption="hORF6" />
-BIOSCI 203 Lab 2 - Protein structure
+== '''BIOSCI 203 Lab 2 - Protein structure''' ==
 ----
-You are viewing a protein structure using the Jmol viewer within Proteopedia. Jmol is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll bar to zoom in and out, and the right mouse button for more options and information.
+On the right-hand side of this page is a view of a protein structure shown using the Jmol viewer within Proteopedia. Jmol is an easy way to view protein structures. Use the left mouse button to rotate the protein model, the middle mouse button or scroll bar to zoom in and out, and the right mouse button for more options and information. Try this out for yourself now ==>
+The protein we will be looking at in this part of the lab is the N-terminal domain of the human 1-Cys peroxidase enzyme hORF6. Click
+<scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>here</scene> for an 'all atoms' view of the protein. This will show us all the atoms (except for the hydrogens) coloured by the 'CPK' colour scheme we talked about in lectures - blue for nitrogen atoms, red for oxygen atoms, grey for carbon atoms and yellow for sulfer atoms. Pretty hard to look at, isn't it?
+We can simplify things by just showing a cartoon that traces the path of the amino acid backbone - α-helices are shown as coils, and β-strands as arrows pointing in the direction of the C-terminus of the protein. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_rainbow/2'>Here</scene> is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. <scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_elements/1'>Here </scene>is a version with the β-strands coloured yellow and the α-helices coloured pink.
-We will be looking at the structure of the N-terminal domain of the human 1-Cys peroxidase enzyme
+It can help to see the
-<scene name='User:J._Shaun_Lott/BIOSCI_203/All_atoms_view/1'>hORF6</scene>.
+<scene name='User:J._Shaun_Lott/BIOSCI_203/Ss_hbonds/1'>backbone hydrogen bonds</scene> that define the secondary structure elements, and sometimes this is clearer shown as a  <scene name='User:J._Shaun_Lott/BIOSCI_203/Backbone_hbonds/1'>C-α trace</scene> rather than a ribbon diagram.