Figure 4.

Binding interactions of the designed stapled peptides (green helix) with ASC^PYD (gray surface) determined from all-atom MD simulations. Two representative peptides ms_ASC^PYD #4 (A) and ms_ASC^PYD #6 (B) are shown. The structures are taken from the end of the 200 ns simulations. Interface residues of the ASC^PYD are marked and colored according to their charges (red = negative, blue = positive, and yellow = hydrophobic). Peptide residues are marked with a prime symbol (´). At the peptide N-terminus, the Arg residue (R’3 or R’1) is involved in stable salt bridge interactions with both Glu13 and Asp48 of ASC^PYD. Two Lys residues (K’6 or K’4; K’11 or K’9) form frequent salt-bridges with residues Asp51, Asp54 and Asp6 of ASC^PYD (see Fig. S1). Phe10 or Ile8 (F’10 or I’8) from the central parts of the peptides are involved in hydrophobic contacts with the side chains of Leu9, Leu50, and Arg5 of ASC^PYD (details in Fig. 5 and S2). Non-specific hydrogen bonds were observed in the simulations between the main-chain of Ser or Val (S’14 or S’12; V’15 or V’13) from the peptide C-terminal and the main-chain of Met1, Gly2 or Arg5 from ASC^PYD. (C and D) Energetic analysis of the MD simulations of the stapled peptide:ASC^PYD complex for two representative peptides ms_ASC^PYD #4 (C) and ms_ASC^PYD #6. (D) Residue-wise binding energy contributions are shown.