Designing an antivenom in 3D (3)
The venom atrolysin
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.
Jou 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: Ca-trace (only the Ca 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?
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.
- Double bonded oxygen atom
- A histidine sidechain
- An alfa helix
The active site
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.
Explain the lock-and-key model
Why is the shape of the enzyme important for binding the substrate>
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.
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.
Locating metal ions is an alternative way to find the active site of enzymes. Take care: there are several other reasons why a metal ion can appear in a 3D structure of a protein, so do not rely blindly on this method to find the active site.
Reset Yasara by clicking File > New and then Yes. Load the file venom2.pdb as you have done.
The zinc ion (Zn2+) is clearly visible as a purple ball in the appropriate representation. Use this ion to find the active site. Cheat: it’s easier to use the sequence bar: Zn is mentioned at the end of the sequence. If you click on Zn while holding the Ctrl key, the protein will automatically rotate so that you can see the ion.