Fig. 4.

Comparison of the 3D-structures for Mini-B (MB) (a) and Super Mini-B (S-MB) (b) in 40% HFIP/60% water determined using molecular dynamics (MD) simulations with preliminary 3D models for KL4 (c) and human SP-C (d). PyMOL representations of backbones are shown as either thick (N- and C-terminal α-helices) ribbons or thin green (extended or turn regions) ribbons; side chains are represented as wireframes. a MD simulation of MB in 40% HFIP/60% water at 100 ns, with the linked Cys-8 and Cys-40 and Cys-11 and Cys-34 (yellow) at the lower left and the turn region (PKGG in green) at the upper right. The N-terminal helix is in the foreground and the C-terminal helix is in the background, with the helical axes nearly parallel. b MD simulation of S-MB in 40% HFIP/60% water at 100 ns, with the extended N-terminal insertion sequence (residues 1-7) in an extended conformation (green) at the lower left and the turn region (PKGG; green) at the upper right. The linked Cys-8 and Cys-40 and Cys-11 and Cys-34 (yellow) are adjacent to the insertion sequence. The N-terminal helix (red ribbon) is in the foreground, and the C-terminal helix (red ribbon) is in the background, with nearly parallel helical axes. c Model of the 21-residue KL4 as an α-helix, with residues 2-20 folding as an α-helix (red ribbon) (see the sections Synthetic Peptides Based on the N- or C-Terminal Domains of SP-B Fold as α-Helical, Amphipathic Domains and Exhibit Surfactant Activities and MD Simulations of MB and S-MB in Lipid-Mimic and Lipid Environments). d Homology model for the 35-residue human SP-C, in which the human sequence is templated onto the 2D-NMR structure of the porcine SP-C (PDB: 1SPF) (see text). The homology-modeled human SP-C folds as an α-helix (red ribbon) for residues 9-33, with residues 1–8 and 33-35 forming extended conformations (green ribbons). Leu-35 is at the lower left, while the N-terminal Leu-1 is at the upper right (see the section MD Simulations of MB and S-MB in Lipid-Mimic and Lipid Environments).