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

ABSTRACT 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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Available from: Durba Sengupta, Aug 30, 2015
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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.
    Journal of Membrane Biology 05/2015; DOI:10.1007/s00232-015-9807-8 · 2.17 Impact Factor
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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.
    Pathogens and Disease 02/2014; 70(3). DOI:10.1111/2049-632X.12151 · 2.55 Impact Factor
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    • "Atomistic simulations were performed to compare MLT properties in different solvent and membrane environments[28] [38] or to compare MLT to other antimicrobial peptides[25]. Both atomistic and coarse-grained simulations were done to investigate spontaneous pore formation [29] [34] [36]. These studies repeatedly concluded that a perfect pore with all MLT peptides being in a perpendicular orientation does not occur spontaneously on a time scale of simulations (tens of microseconds in coarse-grained simulations). "
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    ABSTRACT: An important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. Experiments measure the fraction of peptides in the surface state and the transmembrane state, but no computational study exists that quantifies the free energy curve for the reorientation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight in understanding the peptide-lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increases. In addition, we study the cooperative effect; specifically we investigate if the reorientation barrier is smaller for a second melittin, given that another neighboring melittin was already in the transmembrane orientation. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect.
    The Journal of Physical Chemistry B 10/2013; 117(43). DOI:10.1021/jp406328d · 3.30 Impact Factor
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