Bacterial exopolysaccharides provide protection against phagocytosis, opsonization, and dehydration and act as a major structural component of the extracellular matrix in biofilms. They contribute to biofilmrelated resistance by acting as a diffusion barrier to positively charged antimicrobial agents including cationic antimicrobial peptides (CAPs). We previously created novel CAPs consisting of a nonamphipathic hydrophobic core flanked by Lys residues and containing a Trp residue in the hydrophobic segment as a fluorescent probe. Peptides of this type above a specific hydrophobicity threshold insert spontaneously into membranes and have antimicrobial activity against Gram-positive and Gram-negative bacteria at micromolar concentrations. Here we show that alginate, a polymer of -Dmannuronate and ␣-L-guluronate secreted by the cystic fibrosis pathogen Pseudomonas aeruginosa, induces an ␣-helical conformation detected by circular dichroism spectroscopy and blue shifts in Trp fluorescence maxima in peptides above the hydrophobicity threshold, changes typically observed upon association of such peptides with nonpolar (membrane) environments. Parallel effects were observed in the archetypical CAPs magainin II amide and cecropin P1. Fluorescence resonance energy transfer studies indicated that alginate induces peptide-peptide association only in peptides above the hydrophobicity threshold, suggesting that the hydrophilic alginate polymer behaves as an "auxiliary membrane" for the bacteria, demonstrating a unique protective role for biofilm matrices against CAPs.Pseudomonas aeruginosa is the predominant respiratory tract pathogen in cystic fibrosis (CF) 1 patients, where chronic infection is due to the bacteria growing as a mucoid biofilm, a state characterized by overproduction of alginate (1-3). Alginate is a secreted extracellular polysaccharide composed of the uronic acid -D-mannuronate and its C-5 epimer ␣-L-guluronate (4), which is partially O-acetylated at the second and/or third position(s) of the D-mannuronate residues. The chronicity of P. aeruginosa infections in CF; its high level intrinsic antimicrobial resistance, a result of the low permeability of its outer membrane to antibiotics and multidrug efflux systems; and its propensity to develop resistance during prolonged antimicrobial therapy have all presented major therapeutic challenges to CF caregivers.Our laboratory has developed a new category of cationic antimicrobial peptides that display antibacterial activity (5). The peptides consist of a nonamphipathic hydrophobic core sequence (11-19 residues) flanked at one or both termini by a number of Lys or Arg residues. These peptides, which were originally designed as transmembrane mimetic model peptides (6, 7), have the prototypic sequence KKAAAXAAAAAX-AAWAAXAAAKKKK-NH 2 with several key features: (i) Ala is the preferred background residue because of its mid-range hydropathy and frequent occurrence in membrane protein transmembrane domains; (ii) a Trp residue is inserted into the hydrophobic segment ...