Question

In the protein adenylate kinase, the C-terminal region is a helical, with the sequence Val-Asp-Asp-Val-Phe-Ser-Gln-Val-Cys-Thr-His-Leu-Asp-Thr-Leu-Lys.

a) Underline the hydrophobic amino acids in the sequence.

b) If you identified the correct amino acids you will notice that there is a periodicity of hydrophobic amino acids. What is this periodicity and why would this occur?

Answer 1

Hydrophobic amino acids are those with side-chains that do not like to reside in a water environment. So the amino acids are buried in the hydrophobic core of the protein or in the lipid portion of the membrane.

A)

adenylate kinase

Val-Asp-Asp-Val-Phe-Ser-Gln-Val-Cys-Thr-His-Leu-Asp-Thr-Leu-Lys.

valine(Val), leucine (Leu), phenylalanine(Phe)

Underlined acids are hydrophobic amino acids.

B)

The periodicity of hydrophobic amino acid residues is the same as the periodicity of the a-helix, i.e., 3.6.

This periodicity would allow formation of a hydrophobic surface on one face of the helix, thus allowing it to fold against another hydrophobic region of the protein