Cellular and Molecular Biology

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Studying Transmembrane Protein Structure: Hydrophobicity Plots


Proteins are composed of specific strings of amino acids. Each amino acid, of 20 used to build every protein of the mammalian proteome, has different structural and chemical properties. For instance, amino acids have varying degrees of hydrophobicity which determine how a protein interacts with lipid membranes.

Charting the hydrophobicity of each amino acid allowed researchers to infer the number of transmembrane domains in a particular protein. Below is hydrophobicity plot from a landmark study on the sequence and structure of the AchR $\gamma$ subunit.

Plot adapted from: Nucleotide and deduced amino acid sequences of Torpedo californica acetylcholine receptor gamma subunit. Claudio T, Ballivet M, Patrick J, Heinemann S. Proc Natl Acad Sci U S A. 1983

According to this plot, how many transmembrane $\alpha$-helices are present?

(Hint: It takes approximately 20 amino acids in an $\alpha$-helix to span the lipid bilayer.)