• Tertiary

Well, so far for playing, now we are going to work with real molecules. Please remember, we don't want you to just answer the questions that were typed, but also the questions that were not typed; like: Does this molecule stick to the rules we gave you in the previous steps of the course? What does this molecule do? Is there any relation between the structure and the function? Which animal is famous for producing this molecule? Which plant secretes this molecule? Can you eat it? What is funny about the co-factor bound to this molecule? Does this molecule have a colour? Do humans have this molecule in their genome too? Etcetera.

And finally, it is useful to remember that 'nature doesn't make mistakes.
So, when you see something that
doesn't make sense in terms of what you learned about amino acids and their
role in proteins, you likely have found something interesting like an active
site, a regulatory site, a ligand binding pocket, etc.

EU name: 3D-404

Erabutoxin

Figure 57. Load 1ERA.pdb in yasara. This is erabutoxin (which animal kills you how quickly with this poison?). The turns between the β-strands aren't all perfect β-turns, but nevertheless you can learn from studying them.

First figure out the biology of things. Try to deduce, using common knowledge about the innate and the adaptive immune system why you cannot immunize against a snake venom. Then think what the body does to (try to) deal with the snake venom after a snake bite. And when that is clear, and discussed with the assistants, go answer the questions and see how beautiful the snake optimized this molecule to deal with homo sapiens' defense systems.

The mode of action of erabutoxin isn't known very well yet, but a good hypothesis seems that it binds to the acetylcholine receptor. Which is the endogenous (=natural) ligand for this receptor? And what is the net charge of that molecule? So which residues could, in terms of charge, take the place of this acetylcholine molecule?

Question 71: First, answer for erabutoxin all questions listed above, i.e. the questions that weren't asked (what does the molecule do with whom, where, and why). Which animal produces erabutoxin? Given its name, I guess it is a toxin... Does this toxin kill me? And if yes how quick, and how? Etcetera. If this was the molecule of research for your master internship (Dutch: master stage), you would probably spend a week with Google, PubMed, MRS, BLAST, etc. So today you can easily spend half an hour, I think.

Question 72: I count five turns in this molecule. You too?
Hint: Remember that turn means chain-reversal.
If you cannot agree that there are five turns, then please discuss this with an assistant.

Question 73: Analyze the sequence patterns of the turns. Anything striking (in other words, do you see things that were discussed in the seminar related to the relation between amino acids and secondary structure, or perhaps you see just the opposite somewhere?)?
Which turn is, in terms of its sequence, very different from all the others?

Feel free to study the erabutoxin video: .

EU name: 3D-405

Flavodoxin

Figure 59. Load 4FXN.pdb in yasara. This is a flavodoxin. These molecules bind a flavo group. In this case we don't know yet where the flavo group is located. But you can find out.

Question 74: Start by, again, answering all questions that were not asked. What does this molecule do, and why and with whom, etcetera. In short, get the biological question sorted out with GOOGLE before trying to answer the molecular question with bioinformatics.

Question 75: We call this flavodoxin structure an α/β motif. Why?

Question 76: Where does the flavo group bind in flavodoxin?
Hint: Look for anomalies in the sequence / structure. The flavo group binds in an active site, and active sites tend to be a bit 'special'.

EU name: 3D-402

Triose phosphate isomerase

Figure 60. Load TIMA.PDB in yasara. This is the A-subunit of triose phosphate isomerase. Now it certainly gets time to familiarize yourself with the many display options yasara has to offer. Look at cartoon and ribbon representation. See if you can colour residue types, etc. Feel free to invest some time here. You will earn it back!

Question 77: Follow the chain from N to C. Do you see any regularities in this TIM-barrel structure?
Hint: Follow the chain and write down in short-hand (just use H,S,L for helix Strand , and Loop) what secondary structure elements you come across. If you find very, very short helices, just call them loop...

Plastocyanin

Figure 61. Load 1PCN.pdb in yasara. Plastocyanin is a copper-containing protein involved in electron-transfer.

Question 78: Look up the function of plastocyanin. What does it do and where does it do that?

Question 79: Describe the active site of plastocyanin. And anything else that is striking.
Hint: This includes, of course, a detailed description of the ion binding site. Think (or look up) what you know about copper, and see if this molecule fulfils your expectations.

EU name: 3D-407

Green Fluorescent Protein

Figure 62. Load GFP.pdb in yasara. Green fluorescent protein is often used as a marker in biology. Just hang it on the N- or C-terminal end of your protein of interest, and you get fluorescence where ever you protein goes in the cell.

Look at the structure and find the co-factor. YASARA is not (yet) smart enough to decide for itself to make covalent bonds between the ligand and the protein, so two bonds will not be visible. You can add these bonds with the Edit>Bond option, but that is much work for little glory.

Question 80: The GFP ligand is made autolytically from its own residues. Any idea which residues? (And remember, Google is your friend).
Ps, do not forget to also answer all questions that have not been asked...

Question 81: What is striking about the shape of the GFP fluorophore?
Hint: Look at just the fuorophore, without anything else visible, and rotate the molecule around so that you realy look from all sides.