Question

Consider the following amino acid sequence, found as part of a larger protein: Pro-Gly-Asp-Val-Gln-Phe-Asp-Ile-Arg-Ala-Asp-Gly

What kind of structure do you expect this peptide segment be a part of?

Where on the protein is this likely to occur?

Answer 1

The sequence consists of mainly hydrophobic amino acid residues and some of the polar charged residues. Beta sheet is a secondary structure of protein mainly made up of large aromatic amino acid residues and beta branched amino acid residues (here valine, isoleucine) as well. Proline and glycine are found on the surface to make extensive contact with a different layer of beta sheet. So this sequence must be a part of a beta helix.

This structure will occur in the core region. As interior is away from the water, it does not interfere the hydrophobic interactions. The charged amino acids have the partner to stabilize the protein structure. So by occurring in the interior, the sequence helps the protein to work and function properly.