Molecular recognition and packing frustration in a helical protein
Fig 4
Residue-specific potential energies for Im9 H1→H2 at = 1.10 nm.
(A) Lennard-Jones (filled) and electrostatic (hashed) potential energies for direct interaction of selected interfacial residue pairs from the native configuration (red) and a nonnative (blue) configuration with H1 rotated by +30°. Pairs with |ΔE| > 1 kJ/mol are circled (S1 Text). (B) Snapshot of H1 (orange) packed against H2 (blue) in the native orientation, superposed with the configuration with a nonnative +30° rotation of H1 (both helices in grey). Sidechains involved in residue pairs with |ΔE| > 1 kJ/mol, identified in (A), are shown as sticks. (C, D) Helical wheels show (C) native and (D) nonnative interactions between residues that contribute to the more favorable (red dashed lines) and more unfavorable (green dashed lines) component binding energies for nonnative than for native packing (see part A). As in Fig 1, amino acid residues on the helical wheels are color coded: grey for charged, yellow for nonpolar, and white for polar residues.