Fig. 1.

LPS recognition by AMPs. a Chemical structure of LPS (left). The chemical structure of LPS is divided into the O-antigen, the polysaccharide core and the lipid A moiety. Molecular structure of LPS based on the LPS 3-dimensional structure (right). LPS structure (without O-antigen) was determined in complex with protein FhuA by X-ray diffraction (1FI1.pdb) [64]. b Molecular structure of LPS-binding AMPs MSI594, pardaxin, lactoferrin and YI12WF. Cationic residues are depicted in blue, polar residues in green, hydrophobic residues in yellow and aromatic residues in red. Side chains for aromatic and cationic residues are depicted in the cartoon model to show their location. Surface models are colored by electrostatic potential, from blue (positive charge) to red (negative charge). c Rational design of new LPS-binding peptides. The scheme shows the steps to design new LPS-binding peptides based on the analysis of detailed molecular information on LPS-polypeptide complexes. The steps include: (1) identification of the pharmacophore, (2) rational design of new peptides that resemble the pharmacophore, and (3) peptide refinement. All molecules were drawn using Pymol (DeLano Scientific).