Question

We are currently performing a project in which we have the partial sequence to a novel protein, and we are responsible for determining its structure, function, and many of its components. We know the domains surrounding this area, but we cannot make sense of what this hydrophobicity plot might lead to. We thought it may be a transmembrane type 4 protein, but it does not have any transmembrane domains. The area maps to a coiled coil structure. Is there any possible explanation for such a perfect repetition in hydrophobicity if we do not have a transmembrane domain?

Answer 1

The protein has a hydrophobic repeat. This suggests that the protein is most likely a transmembrane protein as the hydrophobic residues will allow it to get embedded in the lipid bilayer. However, as mentioned, the protein is not transmembrane.

The reason for the regular hydrophobicity can then be linked to the role of the protein. If the protein tends to form homodimers or homotrimers, these hydrophobic repetition sequences might help in holding this protein complex together.

Thus, the repeating hydrophobicity suggest that the protein exists in a complex.