Epsilon Subunit of the E. coli ATP Synthase (1aqt)

Questions to be answered from the Chime exercise.

1. Describe the secondary structure of this two-domain protein.
2. How many H-bonds are shown? What are the patterns? Are they all i(C=O) to i+4(NH) ?
3. This is one of the beta-hairpins. Are the strands parallel or anti-parallel? Can you find an irregularity? What might you call it?
4. This is another beta hairpin. Which side of the sheet is most likely exposed to solvent, top or bottom? Why? How many residues are found in the turn? Explain.
5. This is another beta hairpin. One of the H-bonds between strands is multi-centered. Describe it.
6. This is one of the two beta sheets. Are all of the strands parallel, or anti-parallel? Explain. If you can find 2 parallel strands describe the H-bonding pattern between them. Is it normal?
7. This is the other beta sheet. Are all of the strands parallel, or anti-parallel? There is one irregularity in H-bonding that involves a Proline. Can you describe it?
8. Can you find the 3 Methionine residues? Which one is most exposed?
9. There are at least two complex or network ion pairs, with 3 or more centers. Find one.
10. Find another ion pair between 2 residues in the same alpha-helix.
11. Find another ion pair between 2 residues in different alpha-helices.
12. Find another ion pair between 2 residues in the same beta-strand.
13. Find another ion pair between 2 residues in different beta-strands.
14. Glycine: Catalog which type of secondary structure these residues are found in.
15. Proline: Catalog which type of secondary structure these residues are found in.
16. Find 3 residues (I, L, V) whose side chains are completely buried. Now find 3 with side chains that are highly exposed. What principle does this violate? How could you justify this violation if you knew that Epsilon interacted with several other proteins?
17. How many Phe residues are there? Are they relatively exposed or buried?
18. Are the Tyr side chains more exposed than Phe? Which Tyr has a side chain that is almost completely buried? Which one has a special role at the interface of the 2 domains of Epsilon?
19.