User:J. Shaun Lott/BIOSCI 203
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BIOSCI 203 Lab 2 - Protein structure
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 structure 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 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 see what's going on, 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. is a version with the cartoon coloured from blue at the N-terminus to red at the C-terminus. is a version with the β-strands coloured yellow and the α-helices coloured pink.
It can help to see the that define the secondary structure elements, and sometimes this is clearer shown as a which just shows links between the Cα atoms, rather than a ribbon diagram.
Q1: How many α-helices are there in this protein?
Q2: How many β-strands make up the β-sheet?
