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A. Initial simulation setup with peptides placed between two bilayers. B. Bridging of proximal leaflets of the two bilayers by BPC194. C. Lipid bulging caused by the action of peptides associated with the bilayers. D. Pre-stalk intermediate accompanied by disordered toroidal pore. E. Close-up of the bridging peptides. F. Close-up of the stalk-pore complex. G–J. Splaying of a lipid during the course of a simulation. The peptides are depicted in pink, the phosphorous atoms in yellow and green respectively and the lipid chains in grey. The water is not shown for clarity. In panel F, the water molecules within the pore in one of the bilayers are shown in blue. The other pore cannot be seen in the zoom-in but is visible in panel D.
Source publication
Membrane active peptides can perturb the lipid bilayer in several ways, such as poration and fusion of the target cell membrane, and thereby efficiently kill bacterial cells. We probe here the mechanistic basis of membrane poration and fusion caused by membrane-active, antimicrobial peptides. We show that the cyclic antimicrobial peptide, BPC194, i...
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The development of antimicrobial peptides as new class of antibiotic agents requires structural characterisation and understanding of their diverse mechanisms of action. As the cyclic hexapeptide cWFW (cyclo(RRRWFW)) does not exert its rapid cell killing activity by membrane permeabilisation, in this study we investigated alternative mechanisms of...
Antimicrobial peptides have attracted considerable attention because of their broad-spectrum antimicrobial activity and their low prognostic to induce antibiotic resistance which is the most common source of failure in bacterial infection treatment along with biofilms. The method to design hybrid peptide integrating different functional domains of...
Citations
... 16,17 However, reports on dual membrane simulations in the presence of viral fusion peptides are limited in number. 25,27,30 Dual membrane simulations with multiple copies of an antimicrobial peptide BPC194 had shown the peptides triggering the formation of a fusion bridge between membranes. 27 In our study, we attempted to mimic the conditions of fusion by placing the biologically relevant trimeric form of FP-L between membrane bilayers. ...
... 25,27,30 Dual membrane simulations with multiple copies of an antimicrobial peptide BPC194 had shown the peptides triggering the formation of a fusion bridge between membranes. 27 In our study, we attempted to mimic the conditions of fusion by placing the biologically relevant trimeric form of FP-L between membrane bilayers. We anticipate that longer simulation periods with multiple trimeric units of the correct FP and larger bilayer patches will be required to visualize subsequent stages in fusion. ...
Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, we attempted to identify the correct fusion peptide region in the Spike protein of SARS-CoV-2 by all-atom molecular dynamics simulations of dual membrane systems with varied oligomeric units of putative candidate peptides. Of all of the systems tested, only a trimeric unit of a 40-amino-acid region (residues 816−855 of SARS-CoV-2 Spike) was effective in triggering the initial stages of
membrane fusion, within 200 ns of simulation time. Association of this trimeric unit with dual membranes resulted in the migration of lipids from the upper leaflet of the lower bilayer toward the lower leaflet of the upper bilayer to create a structural unit reminiscent of a fusion bridge. We submit that residues 816−855 of Spike represent the bona fide fusion peptide of SARS-CoV-2 and that computational methods represent an effective way to identify fusion peptides in viral glycoproteins.
... [97] These findings are in agreement with previous studies demonstrating fusogenic properties of host defence peptides, and of parallel fusion and disruption mechanisms. [98,99] 2.6. AMPs as line-active agents AFM proves to make significant contributions into a better understanding of how peptides can stabilise, create and expand membrane edges by lowering the line tension. ...
Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.
... AMPs have been seen to possess antimicrobial properties and could possibly mitigate the limitations of conventional antibiotics Mohamed et al. 2016;Mishra et al. 2017;Young-Speirs et al. 2018). The warranted attraction towards AMPs is due to their capability to alter the conformational integrity and penetrability of bacterial cell membranes by triggering membrane disruption, fusion, or translocation (Moiset et al. 2013). These AMPs tend to be amphipathic with a high positive zeta potential due to the distribution of charged amino acids in their chain (Irazazabal et al. 1858). ...
Antimicrobial peptides (AMPs) have the ability to penetrate as well as transport cargo across bacterial cell membranes, and they have been labeled as exceptional candidates to function in drug delivery. The aim of this study was to investigate the effectiveness of novel formulation of AMPs for enhanced MRSA activity. The strategy was carried out through the formulation of liposomes by thin-layer film hydration methodology, containing phosphatidylcholine, cholesterol, oleic acid, the novel AMP, as well as vancomycin (VCM). Characterization of the AMPs and liposomes included HPLC and LCMS for peptide purity and mass determination; DLS (size, polydispersity, zeta potential), TEM (surface morphology), dialysis (drug release), broth dilution, and flow cytometry (antibacterial activity); MTT assay, haemolysis and intracellular antibacterial studies. The size, PDI, and zeta potential of the drug-loaded AMP2-Lipo-1 were 102.6 ± 1.81 nm, 0.157 ± 0.01, and − 9.81 ± 1.69 mV, respectively, while for AMP3-Lipo-2 drug-loaded formulation, it was 146.4 ± 1.90 nm, 0.412 ± 0.05, and − 4.27 ± 1.25 mV respectively at pH 7.4. However, in acidic pH for both formulations, we observed an increase in size, PDI, and a switch to positive zeta potential, which indicated the pH responsiveness of our liposomal systems. The in vitro drug release studies demonstrated that liposomal formulations released VCM-HCl at a faster rate at pH 6.0 compared to pH 7.4. In vitro antibacterial activity against S. aureus and MRSA revealed that liposomes had enhanced activity at pH 6 compared to pH 7.4. The study revealed that the formulation can potentially be used to enhance activity and penetration of AMPs, thereby improving the treatment of bacterial infections.
... A number of researchers 537,577−579 investigated the ability of small amphipatic peptides, including HA fusion peptides, to stabilize cubic phases and stalk/pore complexes that are relevant as fusion intermediates. Moiset et al. 580 found that certain AMPs, that are traditionally associated with forming transmembrane pores, can also induce stalk formation between juxtaposed membranes. Stalk formation in this case is initiated by the ability of multiple lysine residues to form a bridge between the apposing bilayers and trigger the flipping of lipid tails between the proximal leaflets. ...
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
... Spherical cell morphology in several Gram negative bacteria caused by lysozyme has been previously reported in the case of E. coli [58] or by combination of lysozyme with high pressure treatments [59]. In addition, the formation of cell aggregates has been reported by treatment with antimicrobial peptides in early stages before the lysis of the cells [60,61]. The above reports support the hypothesis that the effect of both, BP100 and lysozyme, may be mainly associated to an alteration of the cell envelope. ...
Background
Fire blight is an important disease affecting rosaceous plants. The causal agent is the bacteria Erwinia amylovora which is poorly controlled with the use of conventional bactericides and biopesticides. Antimicrobial peptides (AMPs) have been proposed as a new compounds suitable for plant disease control. BP100, a synthetic linear undecapeptide (KKLFKKILKYL-NH2), has been reported to be effective against E. amylovora infections. Moreover, BP100 showed bacteriolytic activity, moderate susceptibility to protease degradation and low toxicity. However, the peptide concentration required for an effective control of infections in planta is too high due to some inactivation by tissue components. This is a limitation beause of the high cost of synthesis of this compound. We expected that the combination of BP100 with lysozyme may produce a synergistic effect, enhancing its activity and reducing the effective concentration needed for fire blight control. ResultsThe combination of a synhetic multifunctional undecapeptide (BP100) with lysozyme produces a synergistic effect. We showed a significant increase of the antimicrobial activity against E. amylovora that was associated to the increase of cell membrane damage and to the reduction of cell metabolism. Combination of BP100 with lysozyme reduced the time required to achieve cell death and the minimal inhibitory concentration (MIC), and increased the activity of BP100 in the presence of leaf extracts even when the peptide was applied at low doses. The results obtained in vitro were confirmed in leaf infection bioassays. Conclusions
The combination of BP100 with lysozyme showed synergism on the bactericidal activity against E. amylovora and provide the basis for developing better formulations of antibacterial peptides for plant protection.
... Simulations conducted with biophysical characterization and molecular-dynamics confirmed this relationship, suggesting that cationic charges and amphipathicity, as well as variety in the secondary structure, rigidity, and size of the AMPs are essential features for the complexity and diversity of the pore structure and activity of peptide on the integrity of target membrane [99,100]. Membrane peculiarities between the bodies (i.e., composition of different phospholipids, presence or absence of sterol, presence of fillers) also confer specificities in regard to interactions with peptides [101]. ...
Plant growth is prone to several unfavorable factors that may compromise or impair development and survival, including abiotic or biotic stressors. Aiming at defending themselves, plants have developed several strategies to survive and adapt to such adversities. Cyclotides are a family of plant-derived proteins that exhibit a diverse range of biological activities including antimicrobial and insecticidal activities that actively participate in plant defense processes. Three main categories of peptides have been described: (i) Cyclotides (ii) Sunflower Trypsin Inhibitor (SFTI) and (iii) peptides MCoTI-I and II, from Momordica cochinchinensis. They comprise proteins of approximately 30 amino acids, containing a head-to-tail cyclized backbone, with three disulfide bonds configured in a cystine knot topology, therefore bearing greater peptide stability. Given their features and multifunctionality, cyclotides stand out as promising sources for the discovery of new antimicrobial agents. The present review describes cyclotide occurrence, abundance and action in plants, also their diversity and evolution. Considerations regarding their use in the context of biomedical and agronomical sciences uses are also presented.
... Recent investigations into these aspects have furnished many interesting observations. Peptides other than AMPs have also been found to affect biological membranes and they are now discussed as a group referred to as membrane-active peptides which, according to their distinct biological functions, are generally classified as antimicrobial (AMP), cell-penetration (CPP) or fusion peptides (Wadhwani et al., 2012;Moiset et al., 2013). AMPs and CPPs are known to have some structural and physicochemical similarities; however, fusogenic peptides tend to possess different features and sequences (Wadhwani et al., 2012). ...
Traditionally, most antibiotics are relatively low molecular weight chemical compounds. Bacteria have shown the ability to acquire resistance to many antibiotics. In nature, on the other hand, there are examples of antibiotics to which resistance has not been developed. This is particularly the case for naturally occurring antimicrobial peptides. In this chapter we discuss antimicrobial peptides and their postulated mechanisms of action, followed by a review of synthetic polymers with structures inspired by biological molecules, particularly antimicrobial peptides. We also review the grafting of polymers onto biomaterials and biomedical devices, so as to generate polymeric antimicrobial coatings.
... Simulations conducted with biophysical characterization and molecular-dynamics confirmed this relationship, suggesting that cationic charges and amphipathicity, as well as variety in the secondary structure, rigidity, and size of the AMPs are essential features for the complexity and diversity of the pore structure and activity of peptide on the integrity of target membrane [99,100]. Membrane peculiarities between the bodies (i.e., composition of different phospholipids, presence or absence of sterol, presence of fillers) also confer specificities in regard to interactions with peptides [101]. ...
Plant growth is prone to several unfavorable factors that may compromise or impair development and survival, including abiotic or biotic stressors. Aiming at defending themselves, plants have developed several strategies to survive and adapt to such adversities. Cyclotides are a family of plant-derived proteins that exhibit a diverse range of biological activities including antimicrobial and insecticidal activities that actively participate in plant defense processes. Three main categories of peptides have been described: (i) Cyclotides (ii) Sunflower Trypsin Inhibitor (SFTI) and (iii) peptides MCoTI-I and II, from Momordica cochinchinensis. They comprise proteins of approximately 30 amino acids, containing a head-to-tail cyclized backbone, with three disulfide bonds configured in a cystine knot topology, therefore bearing greater peptide stability. Given their features and multifunctionality, cyclotides stand out as promising sources for the discovery of new antimicrobial agents. The present review describes cyclotide occurrence, abundance and action in plants, also their diversity and evolution. Considerations regarding their use in the context of biomedical and agronomical sciences uses are also presented.
... It is possible that our observed sublinear n 0 dependence is en route to such a linear dependence, but we do not reach high enough inoculum concentrations to observe it. On the other hand, a speculative explanation for a sublinear dependence at all n 0 is that cells aggregate at high densities and high peptide concentrations, 9 which may (Moiset et al. 2013) allow peptide molecules or complexes to affect two cells simultaneously. ...
We measured the minimum inhibitory concentration (MIC) of the antimicrobial peptide pexiganan acting on
Escherichia coli
, and found an intrinsic variability in such measurements. These results led to a detailed study of the effect of pexiganan on the growth curve of E. coli, using a plate reader and manual plating (i.e. time-kill curves). The measured growth curves, together with single-cell observations and peptide depletion assays, suggested that addition of a sub-MIC concentration of pexiganan to a population of this bacterium killed a fraction of the cells, reducing peptide activity during the process, while leaving the remaining cells unaffected. This pharmacodynamic hypothesis suggests a considerable inoculum effect, which we quantified. Our results cast doubt on the use of the MIC as ‘a measure of the concentration needed for peptide action’ and show how ‘coarse-grained’ studies at the population level give vital information for the correct planning and interpretation of MIC measurements.
... Cryogenic transmission electron microscopy (Cryo-TEM) was performed as described in Ref. [3]. Briefly, samples were placed on holey carbon-coated grids (Quantifoil 3.1/1), blotted and vitrified using a Vitrobot (FEI, Eindhoven, The Netherlands). ...
This article contains original data, figures and methods used in the characterization of the liposomal carrier ‘DDC642’ for topical applications, described in “An elastic liposomal formulation for RNAi-based topical treatment of skin disorders: proof-of-concept in the treatment of psoriasis” (Desmet et al., 2016) [1]. Several elastic liposomal formulations have been evaluated for their ability to encapsulate and deliver RNA interference (RNAi) molecules to cultured primary skin cells. The efficiency and effectiveness of these liposomes were compared to that of our previously characterized liposomes, the ‘SECosomes’ (SEC) (Geusens et al., 2010) [2]. After selection of a potential superior carrier, based on encapsulation and transfection efficiency data (Desmet et al., 2016) [1], the selected DDC642 liposomes were characterized more in-depth. Herein, a detailed characterization of the DDC642 liposome and RNAi-loaded lipoplexes is given, including the matching protocols.
