A model for hydrophobic protrusions on peripheral membrane proteins
Fig 7
Protruding hydrophobes predict experimentally verified binding sites.
The figure shows comparisons of predicted binding residues (‘the Likely Inserted Hydrophobe’) with experimentally verified binding sites for a manually curated dataset of 24 proteins (listed in S2 Table). The vertical axis corresponds to values of the angle (Eq 11) comparing the two vectors connecting the center of the protein with either the predicted or known binding sites. Smaller angles imply better agreement between prediction and experiment. Asterisks (*) mark proteins where the Likely Inserted Hydrophobe is an amino acid experimentally identified to be interacting with the membrane. The grey boxplots show the distribution of angles when the known binding site residues are compared to all protruding amino acids on the protein. 1iaz is analysed in its soluble monomeric state, while it forms a transmembrane pore upon oligomerisation. The structure of the Bovine α-lactalbumin (PDBID: 1F6S) has no identified protruding hydrophobes and is marked with a cross at 180°.