Toroidal pores formed by antimicrobial peptides show significant disorder

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 07/2008; 1778(10):2308-17. DOI: 10.1016/j.bbamem.2008.06.007
Source: PubMed


A large variety of antimicrobial peptides have been shown to act, at least in vitro, by poration of the lipid membrane. The nanometre size of these pores, however, complicates their structural characterization by experimental techniques. Here we use molecular dynamics simulations, to study the interaction of a specific class of antimicrobial peptides, melittin, with a dipalmitoylphosphatidylcholine bilayer in atomic detail. We show that transmembrane pores spontaneously form above a critical peptide to lipid ratio. The lipid molecules bend inwards to form a toroidally shaped pore but with only one or two peptides lining the pore. This is in strong contrast to the traditional models of toroidal pores in which the peptides are assumed to adopt a transmembrane orientation. We find that peptide aggregation, either prior or after binding to the membrane surface, is a prerequisite to pore formation. The presence of a stable helical secondary structure of the peptide, however is not. Furthermore, results obtained with modified peptides point to the importance of electrostatic interactions in the poration process. Removing the charges of the basic amino-acid residues of melittin prevents pore formation. It was also found that in the absence of counter ions pores not only form more rapidly but lead to membrane rupture. The rupture process occurs via a novel recursive poration pathway, which we coin the Droste mechanism.

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    • "The precise mode of action in which AMPs enter spontaneously across the microbial membranes has not been determined. On the other hand, several models, such as the transient pore formation [22], lipid phase boundary defects [23] and the disordered toroidal pore formation [24] [25], have been proposed. The internalized peptides inhibit or kill bacterial cells by inhibiting macromolecules synthesis, chaperone-mediated protein folding, cell wall synthesis, and cytoplasmic membrane septum formation. "
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    ABSTRACT: An antimicrobial peptide (AMP), Hn-Mc, was designed by combining the N-terminus of HPA3NT3 and the C-terminus of melittin. This chimeric AMP exhibited potent antibacterial activity with low minimal inhibitory concentrations (MICs), ranging from 1 to 2 μM against four drug-susceptible bacteria and ten drug-resistant bacteria. Moreover, the hemolysis and cytotoxicity was reduced significantly compared to those of the parent peptides, highlighting its high cell selectivity. The morphological changes in the giant unilamellar vesicles and bacterial cell surfaces caused by the Hn-Mc peptide suggested that it killed the microbial cells by damaging the membrane envelope. An in vivo study also demonstrated the antibacterial activity of the Hn-Mc peptide in a mouse model infected with drug-resistant bacteria. In addition, the chimeric peptide inhibited the expression of lipopolysaccharide (LPS)-induced cytokines in RAW264.7 cells by preventing the interaction between LPS and Toll-like receptors. These results suggest that this chimeric peptide is an antimicrobial and anti-inflammatory candidate as a pharmaceutic agent. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · May 2015 · Biochemical and Biophysical Research Communications
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    • "However, still neither peptide insertion nor pore formation is observed over 3–4 ls. This contrasts with some prior simulation studies on related AMPs (Irudayam and Berkowitz 2011; Leontiadou et al. 2006; Manna and Mukhopadhyay 2009; Sengupta et al. 2008), where pore formation was observed in only a few tens of nanoseconds, *100 times shorter than our simulations here. We have recently shown that simulations of AMPs can be poorly converged and depend highly on the chosen force field (Wang et al. 2014), so these earlier results are likely biased toward specific initial arrangement or incorrect. "
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    ABSTRACT: The membrane disruption and pore-forming mechanism of melittin has been widely explored by experiments and computational studies. However, the precise mechanism is still enigmatic, and further study is required to turn antimicrobial peptides into future promising drugs against microbes. In this study, unbiased microsecond (µs) time scale (total 17 µs) atomistic molecular dynamics simulation were performed on multiple melittin systems in 1,2-dimyristoyl-sn-glycero-3-phosphocholine membrane to capture the various events during the membrane disorder produced by melittin. We observed bent U-shaped conformations of melittin, penetrated deeply into the membrane in all simulations, and a special double U-shaped structure. However, no peptide transmembrane insertion, nor pore formation was seen, indicating that these processes occur on much longer timescales, and suggesting that many prior computational studies of melittin were not sufficiently unbiased.
    Full-text · Article · May 2015 · Journal of Membrane Biology
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    • "This has led to a reassessment of the commonly accepted 'toroidal-pore' model, which in the original formulation assumed pores formed by symmetrically arranged peptides interacting with the lipid head groups. Disordered toroidal pores were also observed in MD simulations of melittin (Sengupta et al., 2008) and cateslytin (Jean-Franc ßois et al., 2008 "
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    ABSTRACT: The treatment of biofilm infections is particularly challenging because bacteria in these conditions become refractory to antibiotic drugs. The reduced effectiveness of current therapies spurs research for the identification of novel molecules endowed with antimicrobial activities and new mechanisms of antibiofilm action. Antimicrobial peptides (AMPs) have been receiving an increasing attention as potential therapeutic agents, since they represent a novel class of antibiotics with a wide spectrum of activity and a low rate in inducing bacterial resistance. Over the past decades a large number of naturally occurring AMPs have been identified or predicted from various organisms as effector molecules of the innate immune system playing a crucial role in the first line of defence. Recent studies have shown the ability of some AMPs to act against microbial biofilms, in particular during early phases of biofilm development. Here we provide a review of the antimicrobial peptides tested on biofilms, highlighting their advantages and disadvantages for prophylactic and therapeutic applications. In addition, we describe the strategies and methods for de novo design of potentially active AMPs and discuss how informatics and computational tools may be exploited to improve antibiofilm effectiveness. This article is protected by copyright. All rights reserved.
    Full-text · Article · Feb 2014 · Pathogens and Disease
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