In the representation that you see now, covalent bonds are shown as short sticks of a specific colour. Explain the difference between the yellow and white bonds using this list of amino acid structures. Answer
The 3D structure shows three of the four different types of interactions that are important for protein folding (see the theory section for more information). These different interactions are represented by green, blue and orange sticks.
You now know enough to look at the venom atrolysin, which may be familiar to you if you did the Murder at the airport practicum. Let's start by loading the 3D structure of the poison.
Reset Yasara by clicking File > New and then Yes.
Now, load the file
venom.pdb via File > Load > PDB file (similar to Exercise 2).
You now see the venom in Ball representation: you can see all atoms (except
the hydrogens) as large balls. This is not a very clear representation. Fortunately, a number of alternative representations exist. You can browse through tem by pushing the F1 through F8 keys on your keyboard:
F1: Ball representation (individual atoms)
F2: Ball-and-stick representation (individual atoms + bonds)
F3: Stick representation (the atoms look like sticks)
F4: Cα-trace (only the Cα are represented, connected with sticks)
F5: Backbone-trace (showing only the backbone, no side chains)
F6: Cartoon representation (secondary structure-elements)
F7: Alternative cartoon representation
F8: Add/Remove the side chains of the residues (the "R" groups) in any other representation
Using F5, F6 and F7 you can easily recognise secondary structure elements. Which secondary
structures match the red and blue parts or the protein? Answer
Find the following five structure-elements: a double bonded oxygen atom, a peptide bond, a histidine side chain, an alpha helix and a
disulfide bond.
Use the appropriate representation of the protein for each element
and write those down.
Example: Double bonded oxygen atom: Ball and stick representation. Answers
We will now look for the active site of the protein. That is where the most important amino acids are located and where the actual
chemical reaction takes place. Unfortunately, we have no mutation study at hand to decide which residues are in the active site, so we will have to find another way.
A characteristic feature of the active site of enzymes is that they (almost) always lye in a cavity
or cleft on the surface of the protein. Therefore, a quick-and-dirty way to find the active site is to look for the largest cavity on the surface of the protein.
Why is the active site usually located in a cavity? Answer
Find the active site by rotating the protein and zooming. Choose the representation that you think is most appropriate. Do not spend more than a minute on this search.
If you haven't found anything after a minute, that is not a big problem. On the next page, we will try another way to find the active site, knowing that many enzymes use metal ions to assist their enzymatic activity.
