Molecular recognition and packing frustration in a helical protein
Fig 1
Schematics of Im9 simulation systems.
(A) Full-length Im9 (PDB ID: 1IMQ [47]). Helices are represented as cylinders. (B-D) Combined helical wheel and cylinder representations of systems wherein H1 packs against (B) H2, (C) H4, or (D) H2, H3, and H4. For each helical wheel, the red arrow indicates the residue closest to the viewer. Energetic effects of translating H1 in the directions of the solid blue arrows are determined with the position(s) and orientation(s) of the opposing helix or helices (cylinders) fixed. To evaluate the energetic consequences of helical rotation and nonnative packing, the fragment depicted by the helical wheel is rotated (dashed arrows) to nonnative orientations with positive (+) and negative (‒) rotation angles. Residues on the helical wheels are colored differently depending on the type of amino acid: charged residues in grey, nonpolar residues in yellow, and polar residues in white.