Structure of antimicrobial peptides and lipid membranes probed by interface-sensitive X-ray scattering

The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation

Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.

Main-Chain Cationic Bile Acid Polymers Mimicking Facially Amphiphilic Antimicrobial Peptides

Antibiotic-resistant bacterial infections have led to an increased demand for antibacterial agents that do not contribute to antimicrobial resistance. Antimicrobial peptides (AMPs) with the facially amphiphilic structures have demonstrated remarkable effectiveness, including the ability to suppress antibiotic resistance during bacterial treatment. Herein, inspired by the facially amphiphilic structure of AMPs, the facially amphiphilic skeletons of bile acids (BAs) are utilized as building blocks to create a main-chain cationic bile acid polymer (MCBAP) with macromolecular facial amphiphilicity via polycondensation and a subsequent quaternization. The optimal MCBAP displays an effective activity against Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and Gram-negative Escherichia coli, fast killing efficacy, superior bactericidal stability in vitro, and potent anti-infectious performance in vivo using the MRSA-infected wound model. MCBAP shows the low possibility to develop drug-resistant bacteria after repeated exposure, which may ascribe to the macromolecular facial amphiphilicity promoting bacterial membrane disruption and the generation of reactive oxygen species. The easy synthesis and low cost of MCBAP, the superior antimicrobial performance, and the therapeutic potential in treating MRSA infection altogether demonstrate that BAs are a promising group of building blocks to mimic the facially amphiphilic structure of AMPs in treating MRSA infection and alleviating antibiotic resistance.

The Interaction of the Transmembrane Domain of SARS-CoV-2 E-Protein with Glycyrrhizic Acid in Lipid Bilayer

The interaction of the transmembrane domain of SARS-CoV-2 E-protein with glycyrrhizic acid in a model lipid bilayer (small isotropic bicelles) is demonstrated using various NMR techniques. Glycyrrhizic acid (GA) is the main active component of licorice root, and it shows antiviral activity against various enveloped viruses, including coronavirus. It is suggested that GA can influence the stage of fusion between the viral particle and the host cell by incorporating into the membrane. Using NMR spectroscopy, it was shown that the GA molecule penetrates into the lipid bilayer in a protonated state, but localizes on the bilayer surface in a deprotonated state. The transmembrane domain of SARS-CoV-2 E-protein facilitates deeper GA penetration into the hydrophobic region of bicelles at both acidic and neutral pH and promotes the self-association of GA at neutral pH. Phenylalanine residues of the E-protein interact with GA molecules inside the lipid bilayer at neutral pH. Furthermore, GA influences the mobility of the transmembrane domain of SARS-CoV-2 E-protein in the bilayer. These data provide deeper insight into the molecular mechanism of antiviral activity of glycyrrhizic acid.

Novel insights in antimicrobial and immunomodulatory mechanisms of action of PepBiotics CR-163 and CR-172

OBJECTIVES

Recently our group developed a novel group of antimicrobial peptides termed PepBiotics, of which peptides CR-163 and CR-172 showed optimized antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus without inducing antimicrobial resistance. In this study, the antibacterial mechanism of action and the immunomodulatory activity of these two PepBiotics was explored.

METHODS

RAW264.7 cells were used to determine the ability of PepBiotics to neutralize LPS-and LTA-induced activation of macrophages. Isothermal titration calorimetry and competition assays with dansyl-labeled polymyxin B determined binding characteristics to LPS and LTA. Combined bacterial killing with subsequent macrophage activation assays was performed to determine so-called silent killing'. Finally, flow cytometry of peptide-treated genetically engineered E. coli,expressing GFP and mCherry in the cytoplasm and periplasm, respectively further established the antimicrobial mechanism of PepBiotics.

RESULTS

Both CR-163 and CR-172 were shown to have broad-spectrum activity against ESKAPE pathogens and E. coli, using a membranolytic mechanism of action. PepBiotics could exothermically bind LPS/LTA and were able to replace polymyxin B. Finally, it was demonstrated that bacteria killed by PepBiotics were less prone to stimulate immune cells, contrary to gentamicin and heat-killed bacteria that still elicited a strong immune response CONCLUSIONS: These studies highlight the multifunctional nature of the two peptide antibiotics as both broad spectrum antimicrobial and immunomodulator. Their ability to kill bacteria and reduce unwanted subsequent immune activation is a major advantage and highlights their potential for future therapeutic use.

Mechanistic Evaluation of Antimicrobial Lipid Interactions with Tethered Lipid Bilayers by Electrochemical Impedance Spectroscopy

There is extensive interest in developing real-time biosensing strategies to characterize the membrane-disruptive properties of antimicrobial lipids and surfactants. Currently used biosensing strategies mainly focus on tracking membrane morphological changes such as budding and tubule formation, while there is an outstanding need to develop a label-free biosensing strategy to directly evaluate the molecular-level mechanistic details by which antimicrobial lipids and surfactants disrupt lipid membranes. Herein, using electrochemical impedance spectroscopy (EIS), we conducted label-free biosensing measurements to track the real-time interactions between three representative compounds—glycerol monolaurate (GML), lauric acid (LA), and sodium dodecyl sulfate (SDS)—and a tethered bilayer lipid membrane (tBLM) platform. The EIS measurements verified that all three compounds are mainly active above their respective critical micelle concentration (CMC) values, while also revealing that GML induces irreversible membrane damage whereas the membrane-disruptive effects of LA are largely reversible. In addition, SDS micelles caused membrane solubilization, while SDS monomers still caused membrane defect formation, shedding light on how antimicrobial lipids and surfactants can be active in, not only micellar form, but also as monomers in some cases. These findings expand our mechanistic knowledge of how antimicrobial lipids and surfactants disrupt lipid membranes and demonstrate the analytical merits of utilizing the EIS sensing approach to comparatively evaluate membrane-disruptive antimicrobial compounds.

1,3 Dialkylated Imidazolium Ionic Liquid Causes Interdigitated Domains in a Phospholipid Membrane

Amphiphilic imidazolium-based ionic liquids (ILs) have proven their efficacy in altering the membrane integrity and dynamics. The present article investigates the phase-separated domains in a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membrane induced by 1,3 dialkylated imidazolium IL. Isotherm measurements on DPPC monolayers formed at the air-water interface have shown a decrease in the mean molecular area with the addition of this IL. The positive value of the excess Gibbs free energy of mixing indicates an unfavorable mixing of the IL into the lipid. This leads to IL-induced phase-separated domains in the multilayer of the lipid confirmed by the occurrence of two sets of equidistance peaks in the X-ray reflectivity data. The electron density profile along the surface normal obtained by the swelling method shows the bilayer thickness of the newly formed IL-rich phase to be substantially lower (∼34 Å) than the DPPC phase (∼45.8 Å). This IL-rich phase has been confirmed to be interdigitated, showing an enhanced electron density in the tail region due to the overlapping hydrocarbon chains. Differential scanning calorimetry measurements showed that the incorporation of IL enhances the fluidity of the lipid bilayer. Therefore, the study indicates the formation of an interdigitated phase with a lower order compared to the gel phase in the DPPC membrane supplemented with the IL.

Strategies for Antimicrobial Peptides Immobilization on Surfaces to Prevent Biofilm Growth on Biomedical Devices

Nosocomial and medical device-induced biofilm infections affect millions of lives and urgently require innovative preventive approaches. These pathologies have led to the development of numerous antimicrobial strategies, an emergent topic involving both natural and synthetic routes, among which some are currently under testing for clinical approval and use. Antimicrobial peptides (AMPs) are ideal candidates for this fight. Therefore, the strategies involving surface functionalization with AMPs to prevent bacterial attachment/biofilms formation have experienced a tremendous development over the last decade. In this review, we describe the different mechanisms of action by which AMPs prevent bacterial adhesion and/or biofilm formation to better address their potential as anti-infective agents. We additionally analyze AMP immobilization techniques on a variety of materials, with a focus on biomedical applications. Furthermore, we summarize the advances made to date regarding the immobilization strategies of AMPs on various surfaces and their ability to prevent the adhesion of various microorganisms. Progress toward the clinical approval of AMPs in antibiotherapy is also reviewed.

Partitioning of a Hybrid Lipid in Domains of Saturated and Unsaturated Lipids in a Model Cellular Membrane

The cellular membranes are composed of hundreds of components such as lipids, proteins, and sterols that are chemically and physically distinct from each other. The lipid-lipid and lipid-protein interactions form domains in this membrane, which play vital roles in membrane physiology. The hybrid lipids (HLs) with one saturated and one unsaturated chain can control the shape and size of these domains, ensuring the thermodynamic stability of a membrane. In this study, the thermodynamics of mixing of a HL and its structural effects on the phase separated domains in a model membrane composed of a saturated and an unsaturated lipid have been investigated. The HL is observed to mix into an unsaturated lipid reducing the Gibbs free energy, whereas the mixing is unfavorable in a saturated lipid. The presence of an HL in an unsaturated lipid tends to increase its area fraction, which is reflected in the enhanced correlation length across the bilayers in a multilayered sample. There is a feeble effect on the domain structure of the saturated lipid due to the presence of the HLs at the phase boundary. This study concludes that the HLs preferentially participate in the unsaturated lipid regions compared to that of a saturated lipid.

Delivery by Dendritic Mesoporous Silica Nanoparticles Enhances the Antimicrobial Activity of a Napsin-Derived Peptide Against Intracellular Mycobacterium tuberculosis

Tuberculosis remains a serious global health problem causing 1.3 million deaths annually. The causative pathogen Mycobacterium tuberculosis (Mtb) has developed several mechanisms to evade the immune system and resistances to many conventional antibiotics, so that alternative treatment strategies are urgently needed. By isolation from bronchoalveolar lavage and peptide optimization, a new antimicrobial peptide named NapFab is discovered. While showing robust activity against extracellular Mtb, the activity of NapFab against intracellular bacteria is limited due to low intracellular availability. By loading NapFab onto dendritic mesoporous silica nanoparticles (DMSN) as a carrier system, cellular uptake, and consequently antimycobacterial activity against intracellular Mtb is significantly enhanced. Furthermore, using lattice light-sheet fluorescence microscopy, it can be shown that the peptide is gradually released from the DMSN inside living macrophages over time. By electron microscopy and tomography, it is demonstrated that peptide loaded DMSN are stored in vesicular structures in proximity to mycobacterial phagosomes inside the cells, but the nanoparticles are typically not in direct contact with the bacteria. Based on the combination of functional and live-cell imaging analyses, it is hypothesized that after being released from the DMSN NapFab is able to enter the bacterial phagosome and gain access to the bacilli.

Discerning perturbed assembly of lipids in a model membrane in presence of violacein

Violacein is a naturally found pigment that is used by some gram negative bacteria to defend themselves from various gram positive bacteria. As a result, this molecule has caught attention for its potential biomedical applications and has already shown promising outcomes as an antiviral, an antibacterial, and an anti-tumor agent. Understanding the interaction of this molecule with a cellular membrane is an essential step to extend its use in the pharmaceutical paradigm. Here, the interaction of violacein with a lipid monolayer formed at the air-water interface is found to depend on electrostatic nature of lipids. In presence of violacein, the two dimensional (2D) pressure-area isotherms of lipids have exhibited changes in their phase transition pressure and in-plane elasticity. To gain insights into the out-of-plane structural organization of lipids in a membrane, X-ray reflectivity (XRR) study on a solid supported lipid monolayer on a hydrophilic substrate has been performed. It has revealed that the increase in membrane thickness is more pronounced in the zwitterionic and positively charged lipids compared to the negatively charged one. Further, the lipid molecules are observed to decrease their tilt angle made with the normal of lipid membrane along with an alteration in their in-plane ordering. This has been quantified by grazing incidence X-ray diffraction (GIXD) experiments on the multilayer membrane formed in an environment with controlled humidity. The structural reorganization of lipid molecules in presence of violacein can be utilized to provide a detailed mechanism of the interaction of this molecule with cellular membrane.

New type of borneol-based fluorine-free superhydrophobic antibacterial polymeric coating

A new type of superhydrophobic borneol-based polymeric coating has been prepared. The chemical composition of the polymer particles was analyzed by Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy, which showed that the polymer did not contain fluorine, which can effectively avoid the cytotoxic risk of fluorine. By dynamic light scattering, scanning electron microscopy, and static contact angle measurement, the contact angle of the prepared coating gradually increased with increasing diameter of the polymer particles, and a superhydrophobic coating surface was finally obtained. Interestingly, after dissolving the superhydrophobic sample with tetrahydrofuran and making it a normal hydrophobic sample, the antiadhesion performance for E. coli was greatly reduced, and it could not effectively prevent E. coli adhesion. In addition, a long-term antiadhesion study of bacteria was performed. The superhydrophobic borneol-based polymer coating showed long-term resistance to E. coli adhesion. Therefore, the excellent antibacterial properties and cell compatibility mean that this series of polymer materials has great potential in the field of biomedicine.

Bridging the Antimicrobial Activity of Two Lactoferricin Derivatives in E. coli and Lipid-Only Membranes

We coupled the antimicrobial activity of two well-studied lactoferricin derivatives, LF11-215 and LF11-324, in Escherichia coli and different lipid-only mimics of its cytoplasmic membrane using a common thermodynamic framework for peptide partitioning. In particular, we combined an improved analysis of microdilution assays with ζ-potential measurements, which allowed us to discriminate between the maximum number of surface-adsorbed peptides and peptides fully partitioned into the bacteria. At the same time, we measured the partitioning of the peptides into vesicles composed of phosphatidylethanolamine (PE), phosphatidylgylcerol (PG), and cardiolipin (CL) mixtures using tryptophan fluorescence and determined their membrane activity using a dye leakage assay and small-angle X-ray scattering. We found that the vast majority of LF11-215 and LF11-324 readily enter inner bacterial compartments, whereas only 1-5% remain surface bound. We observed comparable membrane binding of both peptides in membrane mimics containing PE and different molar ratios of PG and CL. The peptides' activity caused a concentration-dependent dye leakage in all studied membrane mimics; however, it also led to the formation of large aggregates, part of which contained collapsed multibilayers with sandwiched peptides in the interstitial space between membranes. This effect was least pronounced in pure PG vesicles, requiring also the highest peptide concentration to induce membrane permeabilization. In PE-containing systems, we additionally observed an effective shielding of the fluorescent dyes from leakage even at highest peptide concentrations, suggesting a coupling of the peptide activity to vesicle fusion, being mediated by the intrinsic lipid curvatures of PE and CL. Our results thus show that LF11-215 and LF11-324 effectively target inner bacterial components, while the stored elastic stress makes membranes more vulnerable to peptide translocation.

Estimation of pore dimensions in lipid membranes induced by peptides and other biomolecules: A review

The cytoplasmic membrane is one of the most frequent cell targets of antimicrobial peptides (AMPs) and other biomolecules. Understanding the mechanism of action of AMPs at the molecular level is of utmost importance for designing of new membrane-specific molecules. In particular, the formation of pores, the structure and size of these pores are of great interest and require nanoscale resolution approaches, therefore, biophysical strategies are essential to achieve an understanding of these processes at this scale. In the case of membrane active peptides, pore formation or general membrane disruption is usually the last step before cell death, and so, pore size is generally directly associated to pore structure and stability and loss of cellular homeostasis, implicated in overall peptide activity. Up to date, there has not been a critical review discussing the methods that can be used specifically for estimating the pore dimensions induced by membrane active peptides. In this review we discuss the scope, relevance and popularity of the different biophysical techniques such as liposome leakage experiments, advanced microscopy, neutron or X-ray scattering, electrophysiological techniques and molecular dynamics studies, all of them useful for determining pore structure and dimension.

Melittin Induces Local Order Changes in Artificial and Biological Membranes as Revealed by Spectral Analysis of Laurdan Fluorescence

Antimicrobial peptides (AMPs) are a class of molecules widely used in applications on eukaryotic and prokaryotic cells. Independent of the peptide target, all of them need to first pass or interact with the plasma membrane of the cells. In order to have a better image of the peptide action mechanism with respect to the particular features of the membrane it is necessary to better understand the changes induced by AMPs in the membranes. Laurdan, a lipid membrane probe sensitive to polarity changes in the environment, is used in this study for assessing changes induced by melittin, a well-known peptide, both in model and natural lipid membranes. More importantly, we showed that generalized polarization (GP) values are not always efficient or sufficient to properly characterize the changes in the membrane. We proved that a better method to investigate these changes is to use the previously described log-normal deconvolution allowing us to infer other parameters: the difference between the relative areas of elementary peak (ΔS_r), and the ratio of elementary peaks areas (R_s). Melittin induced a slight decrease in local membrane fluidity in homogeneous lipid membranes. The addition of cholesterol stabilizes the membrane more in the presence of melittin. An opposite response was observed in the case of heterogeneous lipid membranes in cells, the local order of lipids being diminished. R_S proved to be the most sensitive parameter characterizing the local membrane order, allowing us to distinguish among the responses to melittin of both classes of membrane we investigated (liposomes and cellular membranes). Molecular simulation of the melittin pore in homogeneous lipid bilayer suggests that lipids are more closely packed in the proximity of the melittin pore (a smaller area per lipid), supporting the experimental observation.

NMR studies on the conformation, stability and dynamics of alamethicin in methanol

Alamethicin is an antibiotic peptide comprising 20 amino acid residues and functions as an ion channel in biological membranes. Natural alamethicins have a variety of amino acid sequences. Two of them, used as a mixed sample in this study, are: UPUAUAQUVUGLUPVUUQQO and UPUAUUQUVUGLUPVUUQQO, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated, only the amino acid at position six differs, and the two alamethicins are referred to as alamethicin-A6 and -U6, respectively. The conformation and thermal stability of alamethicin-A6 and -U6 in methanol were examined using proton nuclear magnetic resonance (NMR) spectroscopy. Both alamethicins form an α-helix between the 2nd and 11th residues. The N-terminal, 19th and C-terminal residues take a non-helical conformation. The structure between the 12th and 18th residues has not been well determined due to the absence of cross peaks in the two-dimensional NMR data. The α-helices are maintained up to 54 °C at least. In contrast to these similarities, it has been found that the length of the α-helix of alamethicin-U6 is somewhat shorter than that of alamethicin-A6, the intra-molecular hydrogen bonds formed by the amide proton of the seventh residue is much more thermally stable for alamethicin-U6 than for alamethicin-A6, and the C-terminal residue of alamethicin-U6 has higher mobility than that of alamethicin-A6. The mobility of the N- and C-terminal residues is discussed on the basis of a model chain which consists of particles connected by rigid links, and the physiological significance of the mobility is emphasized.

14-Residue peptaibol velutibol A from Trichoderma velutinum: its structural and cytotoxic evaluation

Velutibol A (1), a new 14-residue peptaibol was isolated from the Himalayan cold habitat fungus Trichoderma velutinum. The structural characterization was carried out by 1D and 2D NMR studies, and tandem mass studies, and Marfey's method aided in determining the stereochemistry of the amino acids. The CD analysis revealed folding of the peptide in a 3₁₀-helical conformation. The intramolecular H-bonding was determined by an NMR-VT experiment. Cytotoxic evaluation was carried out against a panel of cancer cell lines. The cell cycle assay was carried out on human myeloid leukaemia (HL-60) cells and revealed the formation of apoptotic bodies and DNA damage in a dose-dependent manner. Three other peptaibols namely velutibol B (2), velutibol C (3), and velutibol D (4) were also isolated in trace amounts from the psychotropic fungus and characterized through tandem mass spectroscopy and Marfey's analysis.

Velutibol A (1), a new 14-residue peptaibol isolated from the Himalayan cold habitat fungus Trichoderma velutinum.

Soyuretox, an Intrinsically Disordered Polypeptide Derived from Soybean (Glycine Max) Ubiquitous Urease with Potential Use as a Biopesticide

Ureases from different biological sources display non-ureolytic properties that contribute to plant defense, in addition to their classical enzymatic urea hydrolysis. Antifungal and entomotoxic effects were demonstrated for Jaburetox, an intrinsically disordered polypeptide derived from jack bean (Canavalia ensiformis) urease. Here we describe the properties of Soyuretox, a polypeptide derived from soybean (Glycine max) ubiquitous urease. Soyuretox was fungitoxic to Candida albicans, leading to the production of reactive oxygen species. Soyuretox further induced aggregation of Rhodnius prolixus hemocytes, indicating an interference on the insect immune response. No relevant toxicity of Soyuretox to zebrafish larvae was observed. These data suggest the presence of antifungal and entomotoxic portions of the amino acid sequences encompassing both Soyuretox and Jaburetox, despite their small sequence identity. Nuclear Magnetic Resonance (NMR) and circular dichroism (CD) spectroscopic data revealed that Soyuretox, in analogy with Jaburetox, possesses an intrinsic and largely disordered nature. Some folding is observed upon interaction of Soyuretox with sodium dodecyl sulfate (SDS) micelles, taken here as models for membranes. This observation suggests the possibility for this protein to modify its secondary structure upon interaction with the cells of the affected organisms, leading to alterations of membrane integrity. Altogether, Soyuretox can be considered a promising biopesticide for use in plant protection.

Understanding interactions of Citropin 1.1 analogues with model membranes and their influence on biological activity

The rapid emergence of resistant bacterial strains has made the search for new antibacterial agents an endeavor of paramount importance. Cationic antimicrobial peptides (AMPs) have the ability to kill resistant pathogens while diminishing the development of resistance. Citropin 1.1 (Cit 1.1) is an AMP effective against a broad range of pathogens. 20 analogues of Cit 1.1 were prepared to understand how sequence variations lead to changes in structure and biological activity. Various analogues exhibited an increased antimicrobial activity relative to Cit 1.1. The two most promising, AMP-016 (W3F) and AMP-017 (W3F, D4R, K7R) presented a 2- to 8-fold increase in activity against MRSA (both = 4 μg/mL). AMP-017 was active against E. coli (4 μg/mL), K. pneumoniae (8 μg/mL), and A. baumannii (2 μg/mL). NMR studies indicated that Cit 1.1 and its analogues form a head-to-tail helical dimer in a membrane environment, which differs from a prior study by Sikorska et al. Active peptides displayed a greater tendency to form α-helices and to dimerize when in contact with a negatively-charged membrane. Antimicrobial activity was observed to correlate to the overall stability of the α-helix and to a positively charged N-terminus. Biologically active AMPs were shown by SEM and flow cytometry to disrupt membranes in both Gram-positive and Gram-negative bacteria through a proposed carpet mechanism. Notably, active peptides exhibited typical serum stabilities and a good selectivity for bacterial cells over mammalian cells, which supports the potential use of Cit 1.1 analogues as a novel broad-spectrum antibiotic for drug-resistant bacterial infections.

Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem

The use of enhanced sampling molecular dynamics simulations to facilitate the folding of proteins is a relatively new approach which has quickly gained momentum in recent years. Accelerated molecular dynamics (aMD) can elucidate the dynamic path from the unfolded state to the near-native state, “flattened” by introducing a non-negative boost to the potential. Alamethicin F30/3 (Alm F30/3), chosen in this study, belongs to the class of peptaibols that are 7–20 residue long, non-ribosomally synthesized, amphipathic molecules that show interesting membrane perturbing activity. The recent studies undertaken on the Alm molecules and their transmembrane channels have been reviewed. Three consecutive simulations of ~900 ns each were carried out where N-terminal folding could be observed within the first 100 ns, while C-terminal folding could only be achieved almost after 800 ns. It took ~1 μs to attain the near-native conformation with stronger potential boost which may take several μs worth of classical MD to produce the same results. The Alm F30/3 hexamer channel was also simulated in an E. coli mimicking membrane under an external electric field that correlates with previous experiments. It can be concluded that aMD simulation techniques are suited to elucidate peptaibol structures and to understand their folding dynamics.

Folding profiles of antimicrobial scorpion venom-derived peptides on hydrophobic surfaces: a molecular dynamics study

Most helical antimicrobial peptides (AMPs) are usually unfolded in aqueous solution; however they acquire their secondary structure in the presence of a hydrophobic environment such as lipid membranes. Being the biological membranes the main target of many AMPs it is necessary to understand their way of action. Pandinin 2 (Pin2) is an alpha-helical AMP isolated from the venom of the African scorpion Pandinus imperator which shows high antimicrobial activity against Gram-positive bacteria and it is less active against Gram-negative bacteria, nevertheless, it has strong hemolytic activity. Its chemically synthesized Pin2GVG analog has low hemolytic activity while keeping its antimicrobial activity. With the aim of exploring the partition and subsequent folding of these peptides, in this work we report the results of extensive molecular dynamics simulations of Pin2 and Pin2GVG peptides in the presence of 2 hydrophobic environments such as dodecyl-phosphocholine (DPC) micelle and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocoline (POPC) membrane. Our results indicate that Pin2 folds in DPC with a 79% of alpha-helical content, which is in agreement with the experimental results, while in POPC it has 62.5% of alpha-helical content. On the other hand, Pin2GVG presents a higher percentage of alpha-helical structure in POPC and a smaller content in DPC when compared with Pin2. These results can help to better choose the starting structures in future molecular dynamics simulations of AMPs, because these peptides can adopt slightly different conformations depending on the hydrophobic environment.Communicated by Ramaswamy H. Sarma.

Role of Transmembrane Potential and Defects on the Permeabilization of Lipid Bilayers by Alamethicin, an Ion-Channel-Forming Peptide

The insertion and ion-conducting channel properties of alamethicin reconstituted into a 1,2-di- O-phytanyl- sn-glycero-3-phosphocholine bilayer floating on the surface of a gold (111) electrode modified with a 1-thio-β-d-glucose (β-Tg) self-assembled monolayer were investigated using a combination of electrochemical impedance spectroscopy (EIS) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS). The hydrophilic β-Tg monolayer separated the bilayer from the gold substrate and created a water-rich spacer region, which better represents natural cell membranes. The EIS measurements acquired information about the membrane resistivity (a measure of membrane porosity), and the PM-IRRAS experiments provided insight into the conformation and orientation of the membrane constituents as a function of the transmembrane potential. The results showed that the presence of alamethicin had a small effect on the conformation and orientation of phospholipid molecules within the bilayer for all studied potentials. In contrast, the alamethicin peptides assumed a surface state, where the helical axes adopted a large tilt angle with respect to the surface normal, at small transmembrane potentials, and inserted into the bilayer at sufficiently negative transmembrane potentials forming pores, which behaved as barrel-stave ion channels for ionic transport across the membrane. The results indicated that insertion of alamethincin peptides into the bilayer was driven by the dipole-field interactions and that the transitions between the inserted and surface states were electrochemically reversible. Additionally, the EIS measurements performed on phospholipid bilayers without alamethicin also showed that the application of negative transmembrane potentials introduces defects into the bilayer. The membrane resistances measured in both the absence and presence of alamethicin show similar dependencies on the electrode potential, suggesting that the insertion of the peptide may also be assisted by the electroporation of the membrane. The findings in this study provide new insights into the mechanism of alamethicin insertion into phospholipid bilayers.

Interplay of entropy and enthalpy in peptide binding to zwitterionic phospholipid membranes as revealed from membrane thinning

Melittin binding affinity enhances linearly with the membrane thermal thinning rate of the three phosphocholine-based ULVs of diCn:1PC.

Structure-informed detection and quantification of peptides in food and biological fluids

Peptides with biological properties, that is, bioactive peptides, are a class of biomolecules whose health-promoting properties are increasingly being exploited in food and health products. However, research on targeted techniques for the detection and quantification of these peptides is still in its infancy. Such information is needed in order to enhance the biological and chemometric characterization of peptides and their subsequent application in the functional food and pharmaceutical industries. In this review, the role of classic techniques such as electrophoretic, chromatographic, and peptide mass spectrometry in the structure-informed detection and quantitation of bioactive peptides are discussed. Prospects for the use of aptamers in the characterization of bioactive peptides are also discussed. PRACTICAL APPLICATIONS: Although bioactive peptides have huge potential applications in the functional foods and health area, there are limited techniques in enhancing throughput detection, quantification, and characterization of these peptides. This review discusses state-of-the-art techniques relevant in complementing bioactive detection and profiling irrespective of the small number of amino acid units. Insights into challenges, possible remedies and prevailing areas requiring thorough research in the extant literature for food chemists and biotechnologists are also presented.

Crabrolin, a natural antimicrobial peptide: structural properties

A joint application of experimental and computational approaches has revealed the exceptionally high attitude of crabrolin, a 13-residue peptide with sequence FLPLILRKIVTAL-NH₂ , to adopt alpha-helix conformation not only in membrane-mimicking solvents but also in the presence of a not negligible amount of water. Our study shows that this propensity essentially resides in the intrinsic thermodynamic stability of alpha-helix conformation whose kinetic stability is drastically reduced in water solvent. Our analysis suggests that this is due to two effects enhanced by water: a more local effect consisting of the demolition of intra-peptide H-bonds, essential for the alpha-helix formation, and a bulk - electrostatic - effect favoring conformational states more polar than alpha-helix. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

One pathogen two stones: are Australian tree frog antimicrobial peptides synergistic against human pathogens?

Antimicrobial peptides (AMPs) may act by targeting the lipid membranes and disrupting the bilayer structure. In this study, three AMPs from the skin of Australian tree frogs, aurein 1.2, maculatin 1.1 and caerin 1.1, were investigated against Gram-negative Escherichia coli, Gram-positive Staphylococcus aureus, and vesicles that mimic their lipid compositions. Furthermore, equimolar mixtures of the peptides were tested to identify any synergistic interactions in antimicrobial activity. Minimum inhibition concentration and minimum bactericidal concentration assays showed significant activity against S. aureus but not against E. coli. Aurein was the least active while maculatin was the most active peptide and some synergistic effects were observed against S. aureus. Circular dichroism experiments showed that, in the presence of phospholipid vesicles, the peptides transitioned from an unstructured to a predominantly helical conformation (>50%), with greater helicity for POPG/TOCL compared to POPE/POPG vesicles. The helical content, however, was less in the presence of live E. coli and S. aureus, 25 and 5%, respectively. Equimolar concentrations of the peptides did not appear to form greater supramolecular structures. Dye release assays showed that aurein required greater concentration than caerin and maculatin to disrupt the lipid bilayers, and mixtures of the peptides did not cooperate to enhance their lytic activity. Overall, aurein, maculatin, and caerin showed moderate synergy in antimicrobial activity against S. aureus without becoming more structured or enhancement of their membrane-disrupting activity in phospholipid vesicles.

Influence of quaternization of ammonium on antibacterial activity and cytocompatibility of thin copolymer layers on titanium

Antimicrobial coatings are able to improve the osseointegration of dental implants. Copolymers are promising materials for such applications due to their combined properties of two different monomers. To investigate the influence of different monomer mixtures, we have been synthesized copolymers of dimethyl (methacryloxyethyl) phosphonate (DMMEP) and dipicolyl aminoethyl methacrylate in different compositions and have them characterized to obtain the r-parameters. Some of the copolymers with different compositions have also been alkylated with 1-bromohexane, resulting in quaternized ammonium groups. The copolymers have been deposited onto titanium surfaces resulting in ultrathin, covalently bound layers. These layers have been characterized by water contact angle measurements and ellipsometry. The influence of quaternary ammonium groups on antibacterial properties and cytocompatibility was studied: Activity against bacteria was tested with a gram positive Staphylococcus aureus strain. Cytocompatibility was tested with a modified LDH assay after 24 and 72 h to investigate adhesion and proliferation of human fibroblast cells on modified surfaces. The copolymer with the highest content of DMMEP showed a good reduction of S. aureus and in the alkylated version a very good reduction of about 95%. On the other hand, poor cytocompatibility is observed. However, our results show that this trend cannot be generalized for this copolymer system.

Antibacterial adhesion of borneol-based polymer via surface chiral stereochemistry

During its adhesion on external surfaces, a cell exhibits obvious inclination to different molecular chirality, which encourages us to develop a new type of antibacterial material catering to the "chiral taste" of bacteria. On the basis of the natural product borneol (a camphane-type bicyclic monoterpene), a series of borneol-based polymer, polyborneolacrylate (PBA), was successfully prepared and showed superior antibacterial adhesion properties resulting from the borneol isomers on material surface. The results of this study reveal that bacteria simply dislike this type of stubborn surface of PBA, and the PBA surface stereochemistry contributes to the interfacial antibacterial activities. The PBA polymers were evaluated as noncytotoxic and can be simply synthesized, demonstrating their great potential for biomedical applications.

Polymeric nanoarchitectures on Ti-based implants for antibacterial applications

Because of the excellent mechanical properties and good biocompatibility, titanium-based metals are widely used in hard tissue repair, especially load-bearing orthopedic applications. However, bacterial infection and complication during and after surgery often causes failure of the metallic implants. To endow titanium-based implants with antibacterial properties, surface modification is one of the effective strategies. Possessing the unique organic structure composed of molecular and functional groups resembling those of natural organisms, functionalized polymeric nanoarchitectures enhance not only the antibacterial performance but also other biological functions that are difficult to accomplish on many conventional bioinert metallic implants. In this review, recent advance in functionalized polymeric nanoarchitectures and the associated antimicrobial mechanisms are reviewed.

Hierarchical, self-similar structure in native squid pen

The structure of native squid pen (gladius) was investigated in two different species on different length scales. By combining microscopy, atomic force microscopy (AFM), and X-ray diffraction, the experiments probed length scales from millimetres down to nanometres. The gladii showed a hierarchical, self-similar structure in the optical experiments with fibres of different size oriented along the long axis of the gladius. The fibre-like structure was reproduced at the nanoscale in AFM measurements and fibres with diameters of 500 μm, 100 μm, 10 μm, 2 μm and 0.2 μm were observed. Their molecular structure was determined using X-ray diffraction. In the squid gladius, the chitin molecules are known to form nano-crystallites of monoclinic lattice symmetry wrapped in a protein layer, resulting in β-chitin nano-fibrils. Signals corresponding to the α-coil protein phase and β-chitin crystallites were observed in the X-ray experiments and their orientation with respect to the fibre-axis was determined. The size of a nano-fibril was estimated from the X-ray experiments to be about 150 × 300 Å. About 100 of these nano-fibrils are needed to form a 0.2 μm thick micro-fibre. We found that the molecular structure is highly anisotropic with ∼90% of the α-coils and β-chitin crystallites oriented along the fibre-axis, indicating a strong correlation between the macroscale structure and molecular orientation.

Interaction of hydrophobic and amphipathic antimicrobial peptides with lipid bicelles

Bicelles are model membrane systems that can be macroscopically oriented in a magnetic field at physiological temperature. The macroscopic orientation of bicelles allows to detect, by means of magnetic resonance spectroscopies, small changes in the order of the bilayer caused by solutes interacting with the membrane. These changes would be hardly detectable in isotropic systems such as vesicles or micelles. The aim of this work is to show that bicelles represent a convenient tool to investigate the behavior of antimicrobial peptides (AMPs) interacting with membranes, using electron paramagnetic resonance (EPR) spectroscopy. We performed the EPR experiments on spin-labeled bicelles using various AMPs of different length, charge, and amphipathicity: alamethicin, trichogin GA IV, magainin 2, HP(2-20), and HPA3. We evaluated the changes in the order parameter of the spin-labeled lipids as a function of the peptide-to-lipid ratio. We show that bicelles labeled at position 5 of the lipid chains are very sensitive to the perturbation induced by the AMPs even at low peptide concentrations. Our study indicates that peptides that are known to disrupt the membrane by different mechanisms (i.e., alamethicin vs magainin 2) show very distinct trends of the order parameter as a function of peptide concentration. Therefore, spin-labeled bicelles proved to be a good system to evaluate the membrane disruption mechanism of new AMPs.

Acyl-chain correlation in membrane fusion intermediates: x-ray diffraction from the rhombohedral lipid phase

We have studied the acyl-chain conformation in stalk phases of model membranes by x-ray diffraction from oriented samples. As an equilibrium lipid phase induced by dehydration, the stalk or rhombohedral phase exhibits lipidic passages (stalks) between adjacent bilayers, representing a presumed intermediate state in membrane fusion. From the detailed analysis of the acyl-chain correlation peak, we deduce the structural parameters of the acyl-chain fluid above, at, and below the transition from the lamellar to rhombohedral state, at the molecular level.

Direct visualization of the alamethicin pore formed in a planar phospholipid matrix

We present direct visualization of pores formed by alamethicin (Alm) in a matrix of phospholipids using electrochemical scanning tunneling microscopy (EC-STM). High-resolution EC-STM images show individual peptide molecules forming channels. The channels are not dispersed randomly in the monolayer but agglomerate forming 2D nanocrystals with a hexagonal lattice in which the average channel-channel distance is 1.90 ± 0.1 nm. The STM images suggest that each Alm is shared between the two adjacent channels. Every channel consists of six Alm molecules. Three or four of these molecules have the hydrophilic group oriented toward the center of the channel allowing for water column formation inside the channel. The dimensions of the central pore in the images are consistent with the dimension of the water column in a model of hexameric pore proposed in the literature. The images obtained in this work validate the barrel-stave model of the pore formed in phospholipid membranes by amphiphatic peptides. They also provide direct evidence for cluster formation by such pores.

Peptide-induced bilayer thinning structure of unilamellar vesicles and the related binding behavior as revealed by X-ray scattering

We have studied the bilayer thinning structure of unilamellar vesicles (ULV) of a phospholipid 1,2-dierucoyl-sn-glycero-3-phosphocholine (di22:1PC) upon binding of melittin, a water-soluble amphipathic peptide. Successive thinning of the ULV bilayers with increasing peptide concentration was monitored via small-angle X-ray scattering (SAXS). Results suggest that the two leaflets of the ULV of closed bilayers are perturbed and thinned asymmetrically upon free peptide binding, in contrast to the centro-symmetric bilayer thinning of the substrate-oriented multilamellar membranes (MLM) with premixed melittin. Moreover, thinning of the melittin-ULV bilayer associates closely with peptide concentration in solution and saturates at ~4%, compared to the ~8% maximum thinning observed for the correspondingly premixed peptide-MLM bilayers. Linearly scaling the thinning of peptide-ULV bilayers to that of the corresponding peptide-MLM of a calibrated peptide-to-lipid ratio, we have deduced the number of bound peptides on the ULV bilayers as a function of free peptide concentration in solution. The hence derived X-ray-based binding isotherm allows extraction of a low binding constant of melittin to the ULV bilayers, on the basis of surface partition equilibrium and the Gouy-Chapman theory. Moreover, we show that the ULV and MLM bilayers of di22:1PC share a same thinning constant upon binding of a hydrophobic peptide alamethicin; this result supports the linear scaling approach used in the melittin-ULV bilayer thinning for thermodynamic binding parameters of water-soluble peptides.

Determining the orientation and localization of membrane-bound peptides

Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.

Antibacterial surfaces developed from bio-inspired approaches

Prevention of bacterial adhesion and biofilm formation on the surfaces of materials is a topic of major medical and societal importance. Various synthetic approaches based on immobilization or release of bactericidal substances such as metal derivatives, polyammonium salts and antibiotics were extensively explored to produce antibacterial coatings. Although providing encouraging results, these approaches suffer from the use of active agents which may be associated with side-effects such as cytotoxicity, hypersensibility, inflammatory responses or the progressive alarming phenomenon of antibiotic resistance. In addition to these synthetic approaches, living organisms, e.g. animals and plants, have developed fascinating strategies over millions of years to prevent efficiently the colonization of their surfaces by pathogens. These strategies have been recently mimicked to create a new generation of bio-inspired biofilm-resistant surfaces. In this review, we discuss some of these bio-inspired methods devoted to the development of antibiofilm surfaces. We describe the elaboration of antibacterial coatings based on natural bactericidal substances produced by living organisms such as antimicrobial peptides, bacteriolytic enzymes and essential oils. We discuss also the development of layers mimicking algae surfaces and based on anti-quorum-sensing molecules which affect cell-to-cell communication. Finally, we report on very recent strategies directly inspired from marine animal life and based on surface microstructuring.

Contrast matching of an Si substrate with polymer films by anomalous dispersion at the SiKabsorption edge

Anomalous dispersion at the SiKabsorption edge has been used to control the reflection from the interface between a film and an Si substrate, which otherwise complicates the nanostructure analysis of such a film, particularly for the soft-matter case, in grazing-incidence small-angle scattering. Such a reflectionless condition has been chosen for a triblock copolymer thin film, and two-dimensional grazing-incidence small-angle scattering patterns were obtained without the effect of the reflection. The present approach is useful for analysing nanostructures without introducing complicated corrections arising from the reflection.

Revisiting peptide amphiphilicity for membrane pore formation

It has previously been shown that an amphipathic de novo designed peptide made of 10 leucines and four phenylalanines substituted with crown ethers induces vesicle leakage without selectivity. To gain selectivity against negatively charged dimyristoylphosphatidylglycerol (DMPG) bilayers, one or two leucines of the peptide were substituted with positively charged residues at each position. All peptides induce significant calcein leakage of DMPG vesicles. However, some peptides do not induce significant leakage of zwitterionic dimyristoylphosphatidylcholine vesicles and are thus active against only bacterial model membranes. The intravesicular leakage is induced by pore formation instead of membrane micellization. Nonselective peptides are mostly helical, while selective peptides mainly adopt an intermolecular β-sheet structure. This study therefore demonstrates that the position of the lysine residues significantly influences the secondary structure and bilayer selectivity of an amphipathic 14-mer peptide, with β-sheet peptides being more selective than helical peptides.

Peptide model helices in lipid membranes: insertion, positioning, and lipid response on aggregation studied by X-ray scattering

Studying membrane active peptides or protein fragments within the lipid bilayer environment is particularly challenging in the case of synthetically modified, labeled, artificial, or recently discovered native structures. For such samples the localization and orientation of the molecular species or probe within the lipid bilayer environment is the focus of research prior to an evaluation of their dynamic or mechanistic behavior. X-ray scattering is a powerful method to study peptide/lipid interactions in the fluid, fully hydrated state of a lipid bilayer. For one, the lipid response can be revealed by observing membrane thickening and thinning as well as packing in the membrane plane; at the same time, the distinct positions of peptide moieties within lipid membranes can be elucidated at resolutions of up to several angstroms by applying heavy-atom labeling techniques. In this study, we describe a generally applicable X-ray scattering approach that provides robust and quantitative information about peptide insertion and localization as well as peptide/lipid interaction within highly oriented, hydrated multilamellar membrane stacks. To this end, we have studied an artificial, designed β-helical peptide motif in its homodimeric and hairpin variants adopting different states of oligomerization. These peptide lipid complexes were analyzed by grazing incidence diffraction (GID) to monitor changes in the lateral lipid packing and ordering. In addition, we have applied anomalous reflectivity using synchrotron radiation as well as in-house X-ray reflectivity in combination with iodine-labeling in order to determine the electron density distribution ρ(z) along the membrane normal (z axis), and thereby reveal the hydrophobic mismatch situation as well as the position of certain amino acid side chains within the lipid bilayer. In the case of multiple labeling, the latter technique is not only applicable to demonstrate the peptide's reconstitution but also to generate evidence about the relative peptide orientation with respect to the lipid bilayer.