Conformation of polymyxin B analogs in DMSO from NMR spectra and molecular modeling

The tertiary structures of two polymyxin analogues: [formula: see text] and [formula: see text] in DMSO, from solid-phase peptide synthesis and aerobic oxidation were determined from two-dimensional NMR spectra and distance geometry calculations followed by restrained molecular dynamics simulation. The backbone of peptide I had a rectangular shape stabilized by at least two hydrogen bonds and the hydrophilic side chains of five lysine residues, and the hydrophobic side chains of Phe and Leu resided at both sides to form an amphiphilic molecule. This amphiphilic structure of I is likely to interact with lipid A mainly via a hydrophobic interaction. Compared with I, peptide II, which lacks three N-terminal amino-acid residues, exhibits neither amphiphilic property nor binding ability with lipid A.