A model for hydrophobic protrusions on peripheral membrane proteins
Fig 1
The definitions of ‘protrusions’ and ‘co-insertable protruding hydrophobes’.
Panel A shows a cartoon representation of the C2 domain of human phospholipase A2 (PDB ID: 1RLW), and panel B shows the convex hull for the same protein. Panel C shows the structure of the ENTH-domain (PDB ID: 1H0A), which contains an amphipatic helix. The corresponding convex hull is shown on panel D. All Cα- and Cβ-atoms are shown as spheres. Hydrophobes are coloured orange. The convex hull for the Cα- and Cβ-atomic coordinates is shown in blue. All spheres visible on the convex hull representation are vertex residues. ‘Protrusions’ are defined as vertex residues with low local protein density, and shown as large grey spheres. ‘Co-insertable protruding hydrophobes’ are protruding hydrophobes that are adjacent vertices of the convex hull and are shown connected by orange lines. Small black spheres are at vertex residues that have high local density, and do therefore not meet the criteria for protrusions.