Fig. 5

The evolved 3D model for B-YL in lipid bilayers after MD simulations. Molecular Dynamics (MD) simulations were carried out on the B-YL peptide. Main-chain folding of the peptide is displayed in ribbon format, with lipids and water omitted for clarity. Here, the green ribbon MD model for B-YL is shown, in which Tyr replaces Cys at residues 8, 11, 34, and 40 of the parent SP-B peptide mimic Super Mini-B (SMB) with purple stick sidechains (6). This 500 ns simulation predicts a helix-hairpin, in which an N-terminal α-helix (i.e., green N-α, residues R12— L21) connects to a C-terminal α-helix (i.e., green C-α, residues P30—L36) via a turn (green residues I22—L29). The B-YL model also predicts flexible coils for the N-terminal insertion (F1—Y11) and the C-terminal (V37—S41) sequences. The B-YL fold is stabilized by a hydrophobic core of clustered Tyr (Y11, Y34 and Y40) linking together the N- and C-helices through noncovalent interactions involving aromatic rings. The parent (Y7) and substituted (Y8, Y11, Y34 and Y40) tyrosines are shown as purple sticks, and are clustered to the right of the figure