Homework 3

1. You can call a a-helix as 3.6₁₃ helix. What can you call a p helix in this kind of nomenclature? What are the n and r parameters for p helices?

A:

4.4₁₆helix n=4.4 r=0.11nm

 

2.

The above figure shows the selected residues with statistically significant positional preferences in helices (colored regions; data taken from Richardson & Richardson, 1988). Please state the reasons that you think each residue has statistically significant preference at its corresponding position.

A:

1. Proteins will be partial plus in N-termini, partial negative in C-termini. Therefore, Asp and Glu are rich in N-termini, and Lys and Arg rich in C-termini.
2. The N-terminal capping box forms hydrogen bonds between side chains of N_capand amide group of N3,and between side chains of N3 and amide group of N_cap. Therefore, amino acids that have side chain carbonyl group are rich in N_cap.
3. The C-terminal capping motifs lead to left handed helix, therefore Gly is more suitable.

3. How does a prolin residue lead to the kink of a-helices?

A:

1. The psi/phi angle of proline itself is not similiar to the psi/phi angles of a-helices
2. The d-carbon of Pro and the b-carbon of proceeding amino acid have steric interference. This makes non-glycine proceeding residue to have (+30 < psi < +180).

4. To test the role of salt bridges between oppositely charged side chains separated by three and four residues in stabilizing the a-helical conformation, two pairs of peptides of the type

AEAAAKEAAAKEAAAKA

AKAAAEKAAAEKAAAEA

 

AEAAKAEAAKAEAAKA Blue: positively charged residues

AKAAEAKAAEAKAAEA red: negatively charged residues

were compared (S. Marqusee and R. L. Baldwin, Proc. Natl. Acad. Sci. USA 84, 8898-8902, 1987). The a -amino and a-carboxyl groups were blocked with acetyl and amide groups, respectively. How would the first and second peptides of each pair be expected to differ in their helicity? What's the reasons for these differences?

A:

• The first pair may form more stable helix.

• The first pair has electronic residues all three residues apart, that makes them to be approximately at the same face of a a-helix. Therefore, the two polypeptides will form helices to stable each others.

5. Ion pairs in proteins involving Arg residues have been observed to be energetically stronger than those involving Lys residues. If this were the case, in what ways might Arg and Lys residues be used differently in proteins? How could this hypothesis be tested? (Hint: D. B. Wigley et al., Biochem. Biophys. Res. Commun. 149, 927-929, 1987)

A:

• Arg may participate in binding reaction.
• Lys may participate in catalytic reaction.

6.

a) This is a schematically drawing of a four-stranded beta sheet. Please indicate the antiparallel and parallel strands.

b) What is the diople moment of a b-sheet? Is it plausible that parallel and antiparallel sheets could have substantially different dipole interactions? (Hint: W. G. Hol et al., Nature 294, 532-536, 1981; P. T. van Duijnen et al., Biopolymers 24, 735-745, 1985)

A:

1. I-II, II-III are antiparallel

   III-IV is parallel

2. The dipole of peptide bonds cooperativly form the dipole of a b-sheet

   There must be different between parallel and antiparallel b-sheet in dipole moment. The dipole in antiparallel b-sheet cancel each others, but result to partial plus in N-termini and partial negative in C-termini in parallel b-sheet.