Question

Hydrophobic residues usually appear at the first and fourth positions in the seven-residue repeats of polypeptides that form coiled coils.

(a) Why do polar or charged residues usually appear in the remaining five positions?

(b) Why is the sequence$\mathbf{\text{Ile–Gln–Glu–Val–Glu–Arg–Asp}}$ more likely than the sequence$\mathbf{\text{Trp–Gln–Glu–Tyr–Glu–Arg–Asp}}$ to appear in a coiled coil?

Short answer

(a) The polar or charged residues usually appear in the remaining five positions due to side chains being exposed to the solvent.

(b) Due to the non-bulkiness of the side chains of the sequence it is more likely to appear in a coiled-coil.

Step-by-step solution

Concept Introduction

A polypeptide is an unbranched, continuous chain of amino acids held together by peptide bonds.The peptide bond joins the carboxyl group of one amino acid to the amine group of the next amino acid to form an amide.

Polar Residues on the Remaining Positions

(a)The remaining side chains are exposed to the solvent making them polar. The first side chains form hydrophobic surfaces as the helices form a coiled coil.

Therefore, exposure to solvent is the main reason.

Sequence to more likely to appear

(b)

The former sequence $\text{Ile–Gln–Glu–Val–Glu–Arg–Asp}$ fit better in a coiled coil as their side chains are not as bulky as Trp and Tyr.

Therefore, $\text{Ile–Gln–Glu–Val–Glu–Arg–Asp}$ appears more likely.