Clustering of anionic lipids away from zwitterionic ones by cationic antimicrobial agents has recently been established as a mechanism of action of natural small, flexible peptides as well as non-natural synthetic peptide mimics. One of the largest classes of antimicrobial peptides are those that form cationic amphipathic helices on membranes and whose toxic action is dependent on the formation of pores in the membrane or through the "carpet" mechanism. We have evaluated the role of anionic lipid clustering for five of these peptides, i.e., MSI-78, MSI-103, MSI-469, MSI-843 and MSI-1254, with different sequences and properties. We determined whether these amphipathic helical cationic antimicrobial peptides cluster anionic lipids from zwitterionic ones and if this property is related to the species specificity of their toxicity. All five of these peptides were capable of lipid clustering, in contrast to the well studied amphipathic helical antimicrobial peptide, magainin 2, which does not. We ascribe this difference to the lower density of positive charges in magainin 2. Peptides which efficiently cluster anionic lipids generally have a ratio of MIC for S. aureus to that for E. coli >1. The addition of an N-terminal octyl chain did not preclude anionic charge clustering, although the ratio of MIC for S. aureus to that for E. coli was somewhat lowered. In most Gram positive bacteria there is a predominance of anionic lipids in the cytoplasmic membrane. In Gram negative bacteria, however, clustering of anionic lipids away from zwitterionic ones is emerging as an important contributing mechanism of bacterial toxicity for some antimicrobial agents.There is much current interest in increasing the therapeutic efficacy of antimicrobial peptides (1-3). A large variety of antimicrobial agents have been designed for this purpose (4) and one of the major groups comprises the cationic, linear peptides that can form amphipathic helices in a membrane environment, the Amphipathic Helical Cationic Antimicrobial Peptides (AHCAPs). Some of these antimicrobial peptides are also of interest because of their anticancer activities (5). This study deals with five different AHCAPs, whose sequences and overall charge at neutral pH are given in Table 1. Some AHCAPs have been shown to damage bacterial membranes by forming pores that can lead to membrane depolarization and even the loss of soluble molecules from the cytoplasm of the cell. A well studied example of a peptide working by this mechanism is provided by magainin 2 (6). Among the peptides used in the current study, MSI-78, an analog of magainin 2, has also been suggested to act by forming a toroidal type pore (7) the location of the peptide in a bilayer (8). It is thus common for amphipathic helical peptides to form pores in membranes. The formation of these pores is coupled with the self-association of many of these peptides in a highly cooperative manner (9) resulting in a high local density of positive charges that could cluster anionic lipids. The phenomenon of cluste...