Structures

Human beings like order in their life. Scientists create this order by cataloging things. Protein scientists catalog proteins in many classes. Several protein classification schemes exist. Take a look at the following sites:

• CATH.
• SCOP.
• DALI.

These sites are on the one hand very similar. They were all initiated in England, they all have a four letter word as name, they all try to classify proteins. Still, there are differences. I suggest you browse a bit through these three systems.

Question 4:

• What do the three systems claim that is their goal or mission statement?
• How do the three systems differ in their top level classification?
• What do the three systems have in common in their top level classification?
• How many different protein families do exist?
• Describe in your own words the Russian Doll effect.
• Where does crambin sit in the three trees?
• Where does triosephosphate isomerase sit in the three trees?
• Where does thermolysin sit in the three trees?

Structural analysis examples

In this section we will analyze the universe of proteins. You will see some molecules that are selected from different families of the protein kingdom. To warm you up for the real work, some simple questions will be asked with each of them. If you paid good attention during Bioinformatics 1, this will be a 'deja vu erlebnis'.

The file you need to download from the exercise section is indicated in brackets in the header of each exercise.

Try to not only answer the question(s) raised with each structure, but also the questions that were not asked. Like what is this molecule? What does it do? Where does it do it and with whom? Is is used medicinally? Do the sequence and the structure explain the function? Etc.

Erabutoxin

Figure 6. 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 venome. Then think what the body does to (try to) deal with the snake venome 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 5: 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 ... 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 6: I count five turns in this molecule. You too?
Hint: Remember that turn means chain-reversal.

Question 7: 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: .

Satellite tobacco necrosis virus (STNV.PDB)

Figure 8. Follow the chain. If you make a linear plot of the sequence, indicate where the β-strands are, and indicate which pairs of strands are hydrogen bonded, it should be possible to come up with an hypothesis about the folding pathway of this protein.

Question 8: Come up with a hypothesis about the folding pathway of the STNV coat protein .

Bovine pancreatic trypsin inhibitor (BPTI.PDB)

Figure 9. Please indicate in the sequence (below) which cysteines are paired. Describe the geometry of one of the three bridges (distances, angles, torsion angles. What does this molecule do? And how does it do it?

         10        20        30        40        50
     .    |    .    |    .    |    .    |    .    |    .
 RPDFCLEPPYTGPCKARIIRYAYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA
     |        |               |       |            |   |

Question 9: BPTI inhibits something. What does it inhibit, how does it do that, and which aspects of the structure seem to have evolved to do this inhibition optimally?

Question 10: If you only had the sequence of BPTI available to you, which options would you, as a bioinformatician, have available to you to determine/predict which cysteines are bridged?

Flavodoxin (4FXN.PDB)

Figure 10. This molecule normally binds a flavo group. Please determine the binding pocket for this group, and list which residues seem most important for binding the flavo group. Dream up a hypothesis about how this molecule 'deals' with its ligand. (Some knowledge about the characteristics of amino acids is required to answer this question; or a good memory).

Question 11: If you only had the the pictures on this page, could you still estimate the location of the 'active site' in 4FXN? And why?

Carboxypeptidase A (5CPA.PDB)

Figure 11. Make a schematic drawing of the 'important' residues in the environment on the catalytic zinc. Concentrate on the geometry of the Zinc ligands. Think about the potentially missing ligands (H2O), if needed.

FV fragment, light and heavy chain of an antibody (1JHL.PDB)

Figure 12. Any idea which are the hyper-variable loops?

Question 12: Pretend we only had the sequence of this antibody and not its structure, how would you figure out then?

Bacteriorhodopsin in purple membrane (2BRD.PDB)

Figure 13. (This is actually a trimer, but you will only see a monomer)! What is funny about the residue distribution (polar/non-polar) in this molecule? How is the proton transported? Which other questions can be asked about this molecule?

Question 13: Look at the PDBREPORT (see the list of useful links for a pointer to the PDBREPORT site) for 2brd. How does this report 'warn' you that 2brd is a membrane protein?