EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site-bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site-bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.

In contrast to the majority of all known cell types, Gram-negative bacteria have a second membrane, the outer membrane, which is an asymmetric bilayer composed of a phospholipid inner leaflet and a glycolipid outer leaflet. The glycolipid layer, in most cases being composed of a lipopolysaccharide (LPS), is the first target for antimicrobial agents. To get a basic understanding of the membrane-forming properties of LPS, we reconstituted monolayers of deep rough mutant LPS from Salmonella enterica serova Minnesota (R595 LPS), its lipid A moiety, and of the synthetic tetraacyl compound 406 (resembling the biosynthetic lipid A precursor IVa) at the air-water interface of a film balance. The liquid-expanded (LE) and liquid-condensed (LC) domains in the coexisting region were investigated with epifluorescence and, after transferring the monolayer onto mica, as a Langmuir-Blodgett film, with atomic force microscopy (AFM). The fluorescence and the AFM images showed identical domain structure. The higher resolution of the AFM images, however, contained more topographic details. Different heights and adhesion forces between the LE and LC domains could be observed. Differences in the adhesion forces between the AFM tip and the sample were determined in the repulsive and the attractive dynamic scanning modes, demonstrating the importance of a careful interpretation of height images. We propose that an increase in the lateral pressure causing the LE-LC transition of the monolayers leads to a reorientation of the molecules due to a tilt angle between the alkyl chains and the diglucosamine backbone. LPS monolayers have been utilized as a simplified reconstitution model of the outer membrane to study the interaction with antimicrobial agents. We investigated the action of the polycationic peptide polymyxin B (PMB) and found dramatic influences on the domain structures.

Defensins represent a major component of innate host defense against bacteria, fungi, and enveloped viruses. One potent defensin found, e.g., in epithelia, is the polycationic human beta-defensin-3 (hBD3). We investigated the role of the lipid matrix composition, and in particular the presence of negatively charged lipopolysaccharides (LPS) from sensitive (Escherichia coli, Salmonella enterica serovar Minnesota) or resistant (Proteus mirabilis) Gram-negative bacteria or of the zwitterionic phospholipids of human cells, in determining the action of polycationic hBD3 on the different membranes, and related to their biological activity. The main focus was directed on data derived from electrical measurements on a reconstitution system of the OM as a planar asymmetric bilayer composed on one side of LPS and on the other of a phospholipid mixture. Our results demonstrate that the antimicrobial activity and the absence of cytotoxicity can be explained by the lipid-specificity of the peptide. A clear correlation between these aspects of the biological activity of hBD3 and its interaction with lipid matrices could be found. In particular, hBD3 could only induce lesions in those membranes resembling the lipid composition of the OM of sensitive bacterial strains. The permeation through the membrane is a decisive first step for the biological activity of many antimicrobial peptides. Therefore, we propose that the lipid-specificity of hBD3 as well as some other membrane-active antimicrobial peptides is important for their activity against bacteria or mammalian cells.

Lipopolysaccharides (LPS; endotoxin) activate immunocompetent cells of the host via a transmembrane signaling process. In this study, we investigated the function of the LPS-binding protein (LBP) in this process. The cytoplasmic membrane of the cells was mimicked by lipid liposomes adsorbed on mica, and the lateral organization of LBP in these membranes and its interaction with LPS aggregates were characterized by atomic force microscopy. Using cantilever tips functionalized with anti-LBP antibodies, single LBP molecules were localized in the membrane at low concentrations. At higher concentrations, LBP formed clusters of several molecules and caused cross-linking of lipid bilayers. The addition of LPS to LBP-containing liposomes led to the formation of LPS domains in the membranes, which could be inhibited by anti-LBP antibodies. Thus, LBP mediates the fusion of lipid membranes and LPS aggregates.Membrane-embedded proteins or serum proteins interacting with membranes very often play a particular role in cell functioning (e.g. in signal transduction induced by various pathogenic factors). In these cases, signaling occurs across the cytoplasmic membrane via one or more transmembrane or membrane-bound proteins. The participating components are usually known; however, their lateral organization and the mechanism of their interaction are unknown.The cell wall of Gram-negative bacteria consists of the cytoplasmic and an additional outer membrane. This outer membrane is an extremely asymmetric bilayer with respect to the lipid composition. The inner leaflet is composed of a phospholipid mixture, and the outer leaflet is composed of glycolipids, in most cases lipopolysaccharide (LPS). 2When released from the bacterial surface into the blood circulation of the host, LPS plays an important role in the pathogenesis and manifestation of Gram-negative inflammation, in general, and of septic shock, in particular. It is therefore also named endotoxin. The important biological aim of this study was to get an understanding of an early step in the activation mechanism of immune cells (mononuclear cells, MNCs) by LPS. A comparison of the capacity of LPS monomers and aggregates to induce cytokines such as tumor necrosis factor-␣ showed that the aggregates play a biologically important role in the initial step of cell activation (1). One important step in the signal transduction process is the interaction between LPS and the acute phase serum protein LPSbinding protein (LBP). LBP is synthesized by hepatocytes (2) and different epithelial cells (3, 4) and has been described in the literature as a shuttle protein for monomers of LPS or lipid A, the endotoxic principle of LPS, toward the surface of MNCs (5-9). Our group provided evidence for binding of LBP to and intercalation into lipid membranes composed of negatively charged phosphatidylserine (PS) or zwitterionic phosphatidylcholine (PC) and also in LPS aggregates by using fluorescence resonance energy transfer and surface plasmon resonance experiments (10). Furthermore, we also p...

Lipopolysaccharides (LPSs) play a dual role as target and as effector molecules. The knowledge of the LPS-induced activation of human immune cells is increasing; however, surprisingly, much less effort seems to be directed towards the understanding of the mechanisms leading to the killing of the bacterial organisms, which eventually results in the release of LPS from the bacterial surface into the blood circulation. We demonstrate mechanisms of interaction of peptides of the innate immune system (e.g. defensins and cathelicidins) as well as of externally administered antibiotics (e.g. Polymyxin B) with Gram-negative bacteria. The main focus is directed on data derived from electrical measurements on a reconstitution system of the outer membrane as an asymmetric bilayer composed on one side of LPS and on the other of phospholipids. All these antimicrobial peptides (AMPs) are membrane-active and induce the permeabilization of the reconstituted membranes by the formation of lesions. We found that differences in the activity of the AMPs against various sensitive and resistant Gram-negative bacteria can be explained solely by variations in the chemical structure of LPS, e.g. in the composition of the sugar head group. A reduction of the net negative charge of LPS is responsible for a reduced interaction with the polycationic AMPs and thus for resistance. A most important side effect of positively charged AMPs is the neutralization of the negatively charged LPS released from the bacterial surface as a consequence of AMP-induced killing.