Specific binding of Ro 09-0198 (cinnamycin) to phosphatidylethanolamine: a thermodynamic analysis

Modeling the Effect on a Novel Fungal Peptaibol Placed in an All-Atom Bacterial Membrane Mimicking System via Accelerated Molecular Dynamics Simulations

We previously reported on a novel peptaibol, named Tripleurin XIIc (TPN), an 18-residue long sequence produced by the fungus Trichoderma pleuroti. We elucidated its 3D structure via classical and accelerated molecular dynamics simulation (aMD) methods and reported the folding dynamics of TPN in water and chloroform solvents. Peptaibols, in general, are insoluble in water, as they are amphipathic and may prefer hydrophobic environments like transmembrane regions. In this study, we attempted to use aMD simulations to model an all-atom bacterial membrane system while placing a TPN molecule in its vicinity. The results highlighted that TPN was able to introduce some disorder into the membrane and caused lipid clustering. It could also enter the transmembrane region from the water-bilayer interface. The structural dynamics of TPN in the transmembrane region revealed a single energetically stable conformation similar to the one obtained from water and chloroform solvent simulations reported by us previously. However, this linear structure was found to be at the local energy minimum (stable) in water but at a metastable intermediate state (higher energy) in chloroform. Therefore, it could be said that the water solvent can be successfully used for folding simulations of peptaibols.

Amyloidogenic 60-71 deletion/ValThr insertion mutation of apolipoprotein A-I generates a new aggregation-prone segment that promotes nucleation through entropic effects

The N-terminal fragment of apolipoprotein A-I (apoA-I), comprising residues 1-83, contains three segments prone to aggregation: residues 14-22, 53-58, and 67-72. We previously demonstrated that residues 14-22 are critical in apoA-I fibril formation while residues 53-58 entropically drove the nucleation process. Here, we investigated the impact of amyloidogenic mutations (Δ60-71/VT, Δ70-72, and F71Y) located around residues 67-72 on fibril formation by the apoA-I 1-83 fragment. Thioflavin T fluorescence assay demonstrated that the Δ60-71/VT mutation significantly enhances both nucleation and fibril elongation rates, whereas the Δ70-72 and F71Y mutations had minimal effects. Circular dichroism measurements and microscopic observations revealed that all variant fragments formed straight fibrils, transitioning from random coils to β-sheet structures. Kinetic analysis demonstrated that primary nucleation is the dominant step in fibril formation, with fibril elongation reaching saturation at high protein concentrations. Thermodynamically, both nucleation and fibril elongation were enthalpically and entropically unfavorable in all apoA-I 1-83 variants, in which the entropic barrier of nucleation was almost eliminated for the Δ60-71/VT variant. Taken together, our results suggest the presence of new aggregation-prone segment in the Δ60-71/VT variant that promotes nucleation through entropic effects.

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.

Development of Duramycin-Based Molecular Probes for Cell Death Imaging

Cell death is involved in numerous pathological conditions such as cardiovascular disorders, ischemic stroke and organ transplant rejection, and plays a critical role in the treatment of cancer. Cell death imaging can serve as a noninvasive means to detect the severity of tissue damage, monitor the progression of diseases, and evaluate the effectiveness of treatments, which help to provide prognostic information and guide the formulation of individualized treatment plans. The high abundance of phosphatidylethanolamine (PE), which is predominantly confined to the inner leaflet of the lipid bilayer membrane in healthy mammalian cells, becomes exposed on the cell surface in the early stages of apoptosis or accessible to the extracellular milieu when the cell suffers from necrosis, thus representing an attractive target for cell death imaging. Duramycin is a tetracyclic polypeptide that contains 19 amino acids and can bind to PE with excellent affinity and specificity. Additionally, this peptide has several favorable structural traits including relatively low molecular weight, stability to enzymatic hydrolysis, and ease of conjugation and labeling. All these highlight the potential of duramycin as a candidate ligand for developing PE-specific molecular probes. By far, a couple of duramycin-based molecular probes such as Tc-99 m-, F-18-, or Ga-68-labeled duramycin have been developed to target exposed PE for in vivo noninvasive imaging of cell death in different animal models. In this review article, we describe the state of the art with respect to in vivo imaging of cell death using duramycin-based molecular probes, as validated by immunohistopathology.

Kinetic and thermodynamic studies of cinnamycin specific-adsorption on PE-Included-Membranes using surface plasmon resonance

The binding of the cinnamycin on the biomimetic membrane was studied with respect to time using the surface plasmon resonance(SPR). The membrane was composed of the inner layer tethered on the gold surface and the outer layer formed on the inner layer, which was at the desired ratio of dioleoylphosphatidylethanolamine(DOPE) to dioleoylphosphatidyl- choline(DOPC). On the bilayer, the cinnamycin solution was injected and showed different behavior of the binding with respect to time up on its concentration. For kinetic analysis, the behavior was converted to the coverage fraction with respect to time, which was ratio to the saturated response of 5 μM cinnamycin solution. The fraction change with respect to time was function of the available-site, which was eventually the subtraction of the fraction from one. With the fitting of the first order of the available site, the rate constant was acquired into 6∼7 × 10^-3 s^-1. Furthermore, the reciprocals of the fraction and the concentration were fitted with the Langmuir adsorption isotherm. From the fitting, the equilibrium constant was between 1 × 10⁷ and 5 × 10⁷ M^-1.

Radiolabeled Peptides for Molecular Imaging of Apoptosis

Apoptosis is a regulated cell death induced by extrinsic and intrinsic stimulants. Tracking of apoptosis provides an opportunity for the assessment of cardiovascular and neurodegenerative diseases as well as monitoring of cancer therapy at early stages. There are some key mediators in apoptosis cascade, which could be considered as specific targets for delivering imaging or therapeutic agents. The targeted radioisotope-based imaging agents are able to sensitively detect the physiological signal pathways which make them suitable for apoptosis imaging at a single-cell level. Radiopeptides take advantage of both the high sensitivity of nuclear imaging modalities and favorable features of peptide scaffolds. The aim of this study is to review the characteristics of those radiopeptides targeting apoptosis with different mechanisms.

Chemical diversity and mode of action of natural products targeting lipids in the eukaryotic cell membrane

Covering: up to 2019Nature furnishes bioactive compounds (natural products) with complex chemical structures, yet with simple, sophisticated molecular mechanisms. When natural products exhibit their activities in cells or bodies, they first have to bind or react with a target molecule in/on the cell. The cell membrane is a major target for bioactive compounds. Recently, our understanding of the molecular mechanism of interactions between natural products and membrane lipids progressed with the aid of newly-developed analytical methods. New technology reconnects old compounds with membrane lipids, while new membrane-targeting molecules are being discovered through the screening for antimicrobial potential of natural products. This review article focuses on natural products that bind to eukaryotic membrane lipids, and includes clinically important molecules and key research tools. The chemical diversity of membrane-targeting natural products and the molecular basis of lipid recognition are described. The history of how their mechanism was unveiled, and how these natural products are used in research are also mentioned.

Analysis of interactions between cinnamycin and biomimetic membranes

The interaction between the cinnamycin and the biomimetic membranes was studied using the atomic force microscope(AFM). The bilayer was composed of the monolayer tethered on the gold surface and the outer layer fused with the vesicles on the monolayer. The vesicles were prepared at the desired ratio of dioleoylphosphatidylethanolamine(DOPE) to dioleoylphosphatidylcholine(DOPC). On the bilayer, the surface force measurement was performed with the cinnamycin immobilized covalently on the tip surface. The immobilization led to the presence of the adhesion, which was found while the tip was retracted from the bilayer. In addition, the magnitude of the adhesive force was changed with respect to the composition of DOPE in the outer layer. The difference in the adhesion may be attributed to the mean-molecular-area of DOPE and the specific-binding density on the outer layer. Furthermore, the analysis of the rupture force with respect to the loading rate indicated that the rupture length was around 0.1∼0.13 nm, which was similar to that of a van der Waals bond.

Interactions of Cinnamycin-Immobilized Gold Nanorods with Biomimetic Membranes

The behavior of the cinnamycin immobilized on the gold nanorod(AuNR) was investigated using surface plasmon resonance(SPR). For the comparison of the immobilized cinnamycin, the study for the free cinnamycin was also conducted. The bilayer was fabricated by tethering 1,2-dipalmitoyl-sn-glycero-3-phosphothioethanols on a gold surface to form a monolayer and then using liposomes to adsorb an outer layer on the tethered-monolayer. The liposomes were prepared with a desired ratio of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine to 1,2-dioleoyl-sn-glycero-3-phosphocholine (0:100, 5:95, 10:90, 20:80, and 30:70). After the cinnamycin was injected on the bilayers, the specific binding between the cinnamycin and the bilayer was monitored with SPR. The inclusion of DOPE in the outer layer clearly led to the specific binding of the cinnamycin on the membranes. Specifically, the binding behavior of the immobilized was different from that of the free. For the free cinnamycin, the binding amount of cinnamycin at 10% was two times more than that at 5%. For the immobilized cinnamycin, the amounts were identical for both compositions. However, the rate was much faster for the immobilized cinnamycin at 10% than 5%, compared to that for the free at both compositions. This difference was attributed to the mean-molecular areas of the cinnamycin and DOPE, and the steric effect of the AuNR. For the effects of the heat and storage, the immobilized enzyme showed less decrease in the relative binding amount than the free one.

Structure and Dynamics of Cinnamycin-Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids

Cinnamycin is a lantibiotic peptide, which selectively binds to and permeabilizes membranes containing phosphatidylethanolamine (PE) lipids. As PE is a major component of many bacterial cell membranes, cinnamycin has considerable potential for destroying these. In this study, molecular dynamics simulations are used to elucidate the structure of a lipid-cinnamycin complex and the origin of selective lipid binding. The simulations reveal that cinnamycin selectively binds to PE by forming an extensive hydrogen-bonding network involving all three hydrogen atoms of the primary ammonium group of the PE head group. The substitution of a single hydrogen atom with a methyl group on the ammonium nitrogen destabilizes this hydrogen-bonding network. In addition to binding the primary ammonium group, cinnamycin also interacts with the phosphate group of the lipid through a previously uncharacterized phosphate-binding site formed by the backbone Phe10-Abu11-Phe12-Val13 moieties (Abu = 1-α-aminobutyric acid). In addition, hydroxylation of Asp15 at Cβ plays a role in selective binding of PE due to its tight interaction with the charged amine of the lipid head group. The simulations reveal that the position and orientation of the peptide in the membrane depend on the type of lipid to which it binds, suggesting a reason for why cinnamycin selectively permeabilizes PE-containing membranes.

Plant cell-surface GIPC sphingolipids sense salt to trigger Ca2+ influx

Salinity is detrimental to plant growth, crop production and food security worldwide. Excess salt triggers increases in cytosolic Ca²⁺ concentration, which activate Ca²⁺-binding proteins and upregulate the Na⁺/H⁺ antiporter in order to remove Na⁺. Salt-induced increases in Ca²⁺ have long been thought to be involved in the detection of salt stress, but the molecular components of the sensing machinery remain unknown. Here, using Ca²⁺-imaging-based forward genetic screens, we isolated the Arabidopsis thaliana mutant monocation-induced [Ca^2+]_i increases 1 (moca1), and identified MOCA1 as a glucuronosyltransferase for glycosyl inositol phosphorylceramide (GIPC) sphingolipids in the plasma membrane. MOCA1 is required for salt-induced depolarization of the cell-surface potential, Ca²⁺ spikes and waves, Na⁺/H⁺ antiporter activation, and regulation of growth. Na⁺ binds to GIPCs to gate Ca²⁺ influx channels. This salt-sensing mechanism might imply that plasma-membrane lipids are involved in adaption to various environmental salt levels, and could be used to improve salt resistance in crops.

Radiosynthesis and preliminary in vivo evaluation of 18F-labelled glycosylated duramycin peptides for imaging of phosphatidylethanolamine during apoptosis

[¹⁸F]-Labelled duramycin derivatives incorporating hydrophilic aminogalacturonic acid moieties were prepared as tracers for in vivo imaging of phosphatidylethanolamine during apoptosis.

Sugar-based bactericides targeting phosphatidylethanolamine-enriched membranes

Anthrax is an infectious disease caused by Bacillus anthracis, a bioterrorism agent that develops resistance to clinically used antibiotics. Therefore, alternative mechanisms of action remain a challenge. Herein, we disclose deoxy glycosides responsible for specific carbohydrate-phospholipid interactions, causing phosphatidylethanolamine lamellar-to-inverted hexagonal phase transition and acting over B. anthracis and Bacillus cereus as potent and selective bactericides. Biological studies of the synthesized compound series differing in the anomeric atom, glycone configuration and deoxygenation pattern show that the latter is indeed a key modulator of efficacy and selectivity. Biomolecular simulations show no tendency to pore formation, whereas differential metabolomics and genomics rule out proteins as targets. Complete bacteria cell death in 10 min and cellular envelope disruption corroborate an effect over lipid polymorphism. Biophysical approaches show monolayer and bilayer reorganization with fast and high permeabilizing activity toward phosphatidylethanolamine membranes. Absence of bacterial resistance further supports this mechanism, triggering innovation on membrane-targeting antimicrobials.

Bacillus anthracis causes the infectious disease anthrax. Here, the authors synthesized deoxy glycosides that are effective against B. anthracis and related bacteria and found that these amphiphilic compounds kill bacteria via an unusual mechanism of action.

Avenues to molecular imaging of dying cells: Focus on cancer

Successful treatment of cancer patients requires balancing of the dose, timing, and type of therapeutic regimen. Detection of increased cell death may serve as a predictor of the eventual therapeutic success. Imaging of cell death may thus lead to early identification of treatment responders and nonresponders, and to “patient‐tailored therapy.” Cell death in organs and tissues of the human body can be visualized, using positron emission tomography or single‐photon emission computed tomography, although unsolved problems remain concerning target selection, tracer pharmacokinetics, target‐to‐nontarget ratio, and spatial and temporal resolution of the scans. Phosphatidylserine exposure by dying cells has been the most extensively studied imaging target. However, visualization of this process with radiolabeled Annexin A5 has not become routine in the clinical setting. Classification of death modes is no longer based only on cell morphology but also on biochemistry, and apoptosis is no longer found to be the preponderant mechanism of cell death after antitumor therapy, as was earlier believed. These conceptual changes have affected radiochemical efforts. Novel probes targeting changes in membrane permeability, cytoplasmic pH, mitochondrial membrane potential, or caspase activation have recently been explored. In this review, we discuss molecular changes in tumors which can be targeted to visualize cell death and we propose promising biomarkers for future exploration.

Assembly and clustering of natural antibiotics guides target identification

Antibiotics are essential for numerous medical procedures, including the treatment of bacterial infections, but their widespread use has led to the accumulation of resistance, prompting calls for the discovery of antibacterial agents with new targets. A majority of clinically approved antibacterial scaffolds are derived from microbial natural products, but these valuable molecules are not well annotated or organized, limiting the efficacy of modern informatic analyses. Here, we provide a comprehensive resource defining the targets, chemical origins and families of the natural antibacterial collective through a retrobiosynthetic algorithm. From this we also detail the directed mining of biosynthetic scaffolds and resistance determinants to reveal structures with a high likelihood of having previously unknown modes of action. Implementing this pipeline led to investigations of the telomycin family of natural products from Streptomyces canus, revealing that these bactericidal molecules possess a new antibacterial mode of action dependent on the bacterial phospholipid cardiolipin.

The increasing role of phosphatidylethanolamine as a lipid receptor in the action of host defence peptides

Host defence peptides (HDPs) are antimicrobial agents produced by organisms across the prokaryotic and eukaryotic kingdoms. Many prokaryotes produce HDPs, which utilise lipid and protein receptors in the membranes of bacterial competitors to facilitate their antibacterial action and thereby survive in their niche environment. As a major example, it is well established that cinnamycin and duramycins from Streptomyces have a high affinity for phosphatidylethanolamine (PE) and exhibit activity against other Gram-positive organisms, such as Bacillus. In contrast, although eukaryotic HDPs utilise membrane interactive mechanisms to facilitate their antimicrobial activity, the prevailing view has long been that these mechanisms do not involve membrane receptors. However, this view has been recently challenged by reports that a number of eukaryotic HDPs such as plant cyclotides also use PE as a receptor to promote their antimicrobial activities. Here, we review current understanding of the mechanisms that underpin the use of PE as a receptor in the antimicrobial and other biological actions of HDPs and describe medical and biotechnical uses of these peptides, which range from tumour imaging and detection to inclusion in topical microbicidal gels to prevent the sexual transmission of HIV.

Understanding Lipid Recognition by Protein-Mimicking Cyclic Peptides

This paper describes our investigation of the structural determinants of a designed cyclic peptide (cLac, cyclic peptide mimicking lactadherin)¹ for phosphatidylserine (PS) recognition. A highly efficient strategy that takes advantage of the native chemical ligation (NCL) chemistry has been developed for the synthesis and labeling of cyclic peptides in general. Ala scanning of the cLac peptide revealed a sophisticated model for PS binding, in which the peptide scaffold assembles multiple polar residues to balance the desolvation and electrostatic interactions (salt bridge and hydrogen bonding) to achieve lipid selectivity. The results suggest that cLac effectively mimics the membrane binding mechanism of the parent protein lactadherin.

Illuminating the lipidome to advance biomedical research: peptide-based probes of membrane lipids

Systematic investigation of the lipidome will reveal new opportunities for disease diagnosis and intervention. However, lipidomic research has been hampered by the lack of molecular tools to track specific lipids of interest. Accumulating reports indicate lipid recognition can be achieved with properly constructed short peptides in addition to large proteins. This review summarizes the key developments of this area within the past decade. Select lantibiotic peptides present the best examples of low-molecular-weight probes of membrane lipids, displaying selectivity comparable to lipid-binding proteins. Designed peptides, through biomimetic approaches and combinational screening, have begun to demonstrate their potential for lipid tracking in cultured cells and even in living organisms. Biophysical characterization of these lipid-targeting peptides has revealed certain features critical for selective membrane binding, including preorganized scaffolds and the balance of polar and nonpolar interactions. The knowledge summarized herein should facilitate the development of molecular tools to target a variety of membrane lipids.

Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein

Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of K_D = 2–20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery.

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A first description of inhibitors that are specific for the CoA binding site of CPT-2.

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Distinct thermodynamic footprints are observed for site-specific inhibitors of CPT-2.

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Thermodynamic characterization of the CPT-2 active site correlates with structural data.

Role of Phospholipids in Endocytosis, Phagocytosis, and Macropinocytosis

Endocytosis, phagocytosis, and macropinocytosis are fundamental processes that enable cells to sample their environment, eliminate pathogens and apoptotic bodies, and regulate the expression of surface components. While a great deal of effort has been devoted over many years to understanding the proteins involved in these processes, the important contribution of phospholipids has only recently been appreciated. This review is an attempt to collate and analyze the rapidly emerging evidence documenting the role of phospholipids in clathrin-mediated endocytosis, phagocytosis, and macropinocytosis. A primer on phospholipid biosynthesis, catabolism, subcellular distribution, and transport is presented initially, for reference, together with general considerations of the effects of phospholipids on membrane curvature and charge. This is followed by a detailed analysis of the critical functions of phospholipids in the internalization processes and in the maturation of the resulting vesicles and vacuoles as they progress along the endo-lysosomal pathway.

Phosphatidylethanolamine binding is a conserved feature of cyclotide-membrane interactions

Cyclotides are bioactive cyclic peptides isolated from plants that are characterized by a topologically complex structure and exceptional resistance to enzymatic or thermal degradation. With their sequence diversity, ultra-stable core structural motif, and range of bioactivities, cyclotides are regarded as a combinatorial peptide template with potential applications in drug design. The mode of action of cyclotides remains elusive, but all reported biological activities are consistent with a mechanism involving membrane interactions. In this study, a diverse set of cyclotides from the two major subfamilies, Möbius and bracelet, and an all-d mirror image form, were examined to determine their mode of action. Their lipid selectivity and membrane affinity were determined, as were their toxicities against a range of targets (red blood cells, bacteria, and HIV particles). Although they had different membrane-binding affinities, all of the tested cyclotides targeted membranes through binding to phospholipids containing phosphatidylethanolamine headgroups. Furthermore, the biological potency of the tested cyclotides broadly correlated with their ability to target and disrupt cell membranes. The finding that a broad range of cyclotides target a specific lipid suggests their categorization as a new lipid-binding protein family. Knowledge of their membrane specificity has the potential to assist in the design of novel drugs based on the cyclotide framework, perhaps allowing the targeting of peptide drugs to specific cell types.

Synthesis-enabled functional group deletions reveal key underpinnings of amphotericin B ion channel and antifungal activities

Amphotericin B is the archetype for small molecules that form transmembrane ion channels. However, despite extensive study for more than five decades, even the most basic features of this channel structure and its contributions to the antifungal activities of this natural product have remained unclear. We herein report that a powerful series of functional group-deficient probes have revealed many key underpinnings of the ion channel and antifungal activities of amphotericin B. Specifically, in stark contrast to two leading models, polar interactions between mycosamine and carboxylic acid appendages on neighboring amphotericin B molecules are not required for ion channel formation, nor are these functional groups required for binding to phospholipid bilayers. Alternatively, consistent with a previously unconfirmed third hypothesis, the mycosamine sugar is strictly required for promoting a direct binding interaction between amphotericin B and ergosterol. The same is true for cholesterol. Synthetically deleting this appendage also completely abolishes ion channel and antifungal activities. All of these results are consistent with the conclusion that a mycosamine-mediated direct binding interaction between amphotericin B and ergosterol is required for both forming ion channels and killing yeast cells. The enhanced understanding of amphotericin B function derived from these synthesis-enabled studies has helped set the stage for the more effective harnessing of the remarkable ion channel-forming capacity of this prototypical small molecule natural product.

Duramycin-induced destabilization of a phosphatidylethanolamine monolayer at the air-water interface observed by vibrational sum-frequency generation spectroscopy

Duramycin is a small tetracyclic peptide which binds specifically to ethanolamine phospholipids (PE). In this study, we used lipid monolayers consisting of 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) and various phosphatidylcholines (PC) to investigate the effect of duramycin on the organization of lipids and its influence on surrounding water molecules, using vibrational sum-frequency generation spectroscopy in conjunction with surface pressure measurements and fluorescence microscopy. The results show that while duramycin has no effect on the PC lipid monolayers, it induces significant disorder of PE molecules and causes an increase of the PE monolayer surface pressure. Duramycin adopts a β-sheet conformation and is well-ordered at the air-water interface as well as after binding to PE. Our results are consistent with duramycin inserting into the PE monolayer via its hydrophobic end, exposing phenylalanine residues to the lipid. Binding of duramycin to PE broadens the hydrogen-bond distribution of lipid-bound water molecules, notably increasing the fraction of the less strongly hydrogen-bonded, possibly undercoordinated, water molecules. Fluorescence microscopy reveals that the interaction of duramycin with PE causes a change in the shape of the liquid-condensed domains of the PE monolayer from circular to horseshoe-like, indicating a reduction of line tension at the boundary of the two lipid phases. These results reveal that the first steps in the disruption of membrane integrity by duramycin consist of a reduction of the line tension, a decrease in the lipid order, and a weakening of the hydrogen bonding network of water around PE.

Isothermal microcalorimetry to investigate non specific interactions in biophysical chemistry

Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.

Visualization of phospholipid particle fusion induced by duramycin

We visualized nanometer-scale phospholipid particle fusion by scanning tunneling microscopy (STM) on an alkanethiol-modified gold substrate, induced by duramycin, a tetracyclic antibiotic peptide with 19 amino residues. Ultrasonic homogenization generated a suspension mainly consisting of minimal lipid particles (MLP) from 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in a phosphate buffer solution, confirmed by dynamic light scattering (DLS). In situ STM discerned individual MLP as particles (diameter approximately 8 nm) spread on Au(111), modified with alkanethiol, within the suspension. The MLP became fragile by the presence of duramycin, and the MLP were easily scratched by the scanning tip into multilayers along the surface. This process of particle fusion on the gold surface coincides with the aggregation of MLP in the suspension, observed by DLS. It was demonstrated that STM is capable of discerning and monitoring the nanometer-scale features of phospholipid particles altered by antibiotics with biochemical impact. STM might allow in situ, real-space, nanometer-scale observations of minute particles composed of phospholipids within the real cells with the highest magnification ratio.

The yeast plasma membrane P4-ATPases are major transporters for lysophospholipids

The transbilayer movement of phospholipids plays an essential role in establishing and maintaining the asymmetric distribution of lipids in biological membranes. The P4-ATPase family has been implicated as the major transporters of the aminoglycerophospholipids in both surface and endomembrane systems. Historically, fluorescent lipid analogs have been used to monitor the lipid transport activity of the P4-ATPases. Recent evidence now demonstrates that lyso-phosphatidylethanolamine (lyso-PtdEtn) and lyso-phosphatidylcholine (lyso-PtdCho) are bona fide biological substrates transported by the yeast plasma membrane ATPases, Dnf1p and Dnf2p, in consort with a second protein Lem3p. Subsequent to transport, the lysophospholipids are acylated by the enzyme Ale1p to produce PtdEtn and PtdCho. The transport of the lysophospholipids occurs at rates sufficient to support all the PtdEtn and PtdCho synthesis required for rapid cell growth. The lysophospholipid transporters also utilize the anti-neoplastic and anti-parasitic ether lipid substrates related to edelfosine. The identification of biological substrates for the plasma membrane ATPases coupled with the power of yeast genetics now provides new tools to dissect the structure and function of the aminoglycerophospholipid transporters.

99mTc-labeled duramycin as a novel phosphatidylethanolamine-binding molecular probe

With only 19 amino acids, duramycin is the smallest known polypeptide that has a defined 3-dimensional binding structure. Duramycin binds phosphatidylethanolamine (PtdE) at a 1:1 ratio with high affinity and exclusive specificity. As an abundant binding target, PtdE is a major phospholipid and accounts for about 20% of the phospholipid content in mammalian cellular membranes. PtdE is externalized to the surface of apoptotic cells and also becomes accessible in necrotic cells because of compromised plasma membrane integrity. Given the unique physicochemical properties of duramycin and the availability of PtdE in acute cell death, the goal of this study was to develop and evaluate 99mTc-duramycin as a novel molecular probe for imaging PtdE.

METHODS

Duramycin is covalently modified with succinimidyl 6-hydrazinonicotinate acetone hydrazone (HYNIC) and labeled with 99mTc using a coordination chemistry involving tricine-phosphine coligands. The retention of PtdE-binding activities was confirmed using competition assays with PtdE-containing liposomes. The blood clearance, pharmacokinetics, and biodistribution of 99mTc-duramycin were measured in rats. Finally, 99mTc-duramycin binding to acute cell death in vivo was demonstrated using a rat model of acute myocardial infarction induced by ischemia and reperfusion and confirmed using autoradiography and histology.

RESULTS

HYNIC-derivatized duramycin with 1:1 stoicheometry was synthesized and confirmed by mass spectrometry. The radiolabeling efficiency was 80%-85%, radiochemical purity was 78%-89%, and specific activity was 54 GBq. The radiotracer was purified with high-performance liquid chromatography radiodetection before use. The specific uptake of 99mTc-duramycin in apoptotic cells, compared with that in viable control cells, was enhanced by more than 30-fold. This binding was competitively diminished in the presence of PtdE-containing liposomes but not by liposomes consisting of other phospholipid species. Intravenously injected 99mTc-duramycin has favorable pharmacokinetic and biodistribution profiles: it quickly clears from the circulation via the renal system, with a blood half-life of less than 4 min in rats. The hepatic and gastrointestinal uptake were very low. 99mTc-duramycin is completely unmetabolized in vivo, and the intact agent is recovered from the urine. Combined with a fast clearance and low hepatic background, the avid binding of 99mTc-duramycin to the infarcted myocardium quickly becomes conspicuous shortly after injection. The uptake of radioactivity in infarcted tissues was confirmed by autoradiography and histology.

CONCLUSION

99mTc-duramycin is a stable, low-molecular-weight PtdE-binding radiopharmaceutical, with favorable in vivo imaging profiles. It is a strong candidate as a molecular probe for PtdE imaging and warrants further development and characterization.

Identification of the receptor-binding sites in the carboxyl-terminal half of the heavy chain of botulinum neurotoxin types C and D

Botulinum neurotoxin (BoNT) binds to presynaptic neuronal cells and blocks neurotransmitter release. The carboxyl-terminal half of the heavy chain (H(C)) of the neurotoxin recognizes its specific receptor on the plasma membrane. We have previously demonstrated that BoNT/C binds to gangliosides GD1b and GT1b under physiological conditions, while BoNT/D interacts with phosphatidylethanolamine (PE). Here we report that the recognition sites for gangliosides and PE are present in the carboxyl-terminal domain of H(C). Chimeric mutants and site-directed mutants of BoNT/C-H(C) and BoNT/D-H(C) were generated and their binding activities evaluated. The chimeric H(C) that consisted of the amino-terminal half of BoNT/D-H(C) and the carboxyl-terminal half of BoNT/C-H(C) possessed activity similar to the authentic BoNT/C-H(C), suggesting that the carboxyl-terminal region of H(C) is involved in the receptor recognition of BoNT/C. Moreover, analysis using site-directed mutants indicated that the peptide motif W(1257)Ycdots, three dots, centeredG(1270)cdots, three dots, centeredH(1282) plays an important role in the interaction between BoNT/C and gangliosides. In contrast, we revealed that two lysine residues of BoNT/D-H(C) are involved in the formation of the critical binding site for receptor binding.

Curvature-dependent recognition of ethanolamine phospholipids by duramycin and cinnamycin

Duramycin is a 19-amino-acid tetracyclic lantibiotic closely related to cinnamycin (Ro09-0198), which is known to bind phosphatidylethanolamine (PE). The lipid specificity of duramycin was not established. The present study indicates that both duramycin and cinnamycin exclusively bind to ethanolamine phospholipids (PE and ethanolamine plasmalogen). Model membrane study indicates that the binding of duramycin and cinnamycin to PE-containing liposomes is dependent on membrane curvature, i.e., the lantibiotics bind small vesicles more efficiently than large liposomes. The binding of the lantibiotics to multilamellar liposomes induces tubulation of membranes, as revealed by electron microscopy and small-angle x-ray scattering. These results suggest that both duramycin and cinnamycin promote their binding to the PE-containing membrane by deforming membrane curvature.

New developments in lantibiotic biosynthesis and mode of action

Lantibiotics are a unique class of peptide antibiotics. Recent studies of the proteins involved in the elaborate post-translational modifications of lantibiotics have revealed that these enzymes have relaxed substrate specificity. These modifications include the dehydration of serine and threonine residues followed by the intramolecular addition of cysteine thiols to the unsaturated amino acids to create an intricate polycyclic peptide. The use of peptide engineering in vivo and in vitro has allowed investigation of their biosynthetic machinery. Several members utilize a unique mode of biological action that involves the sequestration of lipid II, a crucial intermediate in peptidoglycan biosynthesis, to form pores in bacterial membranes.

Temperature dependence of the binding of endotoxins to the polycationic peptides polymyxin B and its nonapeptide

The interaction between endotoxins-free lipid A and various lipopolysaccharide (LPS) chemotypes with different sugar chain lengths-and the polycationic peptides polymyxin B and polymyxin nonapeptide has been investigated by isothermal titration calorimetry between 20 and 50 degrees C. The results show a strong dependence of the titration curves on the phase state of the endotoxins. In the gel phase (<30 degrees C for LPS and <45 degrees C for lipid A), an endothermic reaction is observed, for which the driving force is an entropically driven endotoxin-polymyxin interaction, due to disruption of the ordered water structure and cation assembly in the lipid A backbone and adjacent molecules. In the liquid crystalline phase (>35 degrees C for LPS and >47 degrees C for lipid A) an exothermic reaction takes place, which is mainly due to the strong electrostatic interaction of the polymyxins with the negative charges of the endotoxins, i.e., the entropic change DeltaS is much lower than in the gel phase. For endotoxins with short sugar chains (lipid A, LPS Re, LPS Rc) the stoichiometry of the polymyxin binding corresponds to pure charge neutralization; for the compounds with longer sugar chains (LPS Ra, LPS S-form) this is no longer valid. This can be related to the lower susceptibility of the corresponding bacterial strains to antibiotics.

Enteropathogenic Escherichia coli infection triggers host phospholipid metabolism perturbations

Enteropathogenic Escherichia coli (EPEC) specifically recognizes phosphatidylethanolamine (PE) on the outer leaflet of host epithelial cells. EPEC also induces apoptosis in epithelial cells, which results in increased levels of outer leaflet PE and increased bacterial binding. Consequently, it is of interest to investigate whether EPEC infection perturbs host cell phospholipid metabolism and whether the changes play a role in the apoptotic signaling. Our findings indicate that EPEC infection results in a significant increase in the epithelial cell PE level and a corresponding decrease in the phosphatidylcholine (PC) level. PE synthesis via both the de novo pathway and the serine decarboxylation pathway was enhanced, and de novo synthesis of phosphatidylcholine via CDP-choline was reduced. The changes were transitory, and the maximum change was noted after 4 to 5 h of infection. Addition of exogenous PC or CDP-choline to epithelial cells prior to infection abrogated EPEC-induced apoptosis, suggesting that EPEC infection inhibits the CTP-phosphocholine cytidylyltransferase step in PC synthesis, which is reportedly inhibited during nonmicrobially induced apoptosis. On the other hand, incorporation of exogenous PE by the host cells enhanced EPEC-induced apoptosis and necrosis without increasing bacterial adhesion. This is the first report that pathogen-induced apoptosis is associated with significant changes in PE and PC metabolism, and the results suggest that EPEC adhesion to a host membrane phospholipid plays a role in disruption of host phospholipid metabolism.

Thermodynamics of lipid–peptide interactions

This review is focused on peptide molecules which exhibit a limited solubility in the aqueous phase and bind to the lipid membrane from the aqueous medium. Surface adsorption, membrane insertion, and specific binding are usually accompanied by changes in the heat content of the system and can be measured conveniently with isothermal titration calorimetry, avoiding the necessity of peptide labeling. The driving forces for peptide adsorption and binding are hydrophobicity, electrostatics, and hydrogen bonding. An exclusively hydrophobic interaction is exemplified by the immunosuppressant drug cyclosporine A. Its insertion into the membrane can be described by a simple partition equilibrium X(b)=K(0)C(eq). If peptide and membrane are both charged, electrostatic interactions are dominant leading to nonlinear binding curves. The concentration of the peptide near the membrane interface can then be much larger than its bulk concentration. Electrostatic effects must be accounted for by means of the Gouy-Chapman theory before conventional binding models can be applied. A small number of peptides and proteins bind with very high affinity to a specific lipid species only. This is illustrated for the lantibiotic cinnamycin (Ro 09-0198) which forms a 1:1 complex with phosphatidyethanolamine with a binding constant of 10(8) M(-1). Membrane adsorption and insertion can be accompanied by conformational transitions facilitated, in part, by hydrogen bonding mechanisms. The two membrane-induced conformational changes to be discussed are the random coil-to-alpha-helix transition of amphipathic peptides and the random coil-to-beta-structure transition of Alzheimer peptides.

A Novel Human Phosphatidylethanolamine-binding Protein Resists Tumor Necrosis Factor α-induced Apoptosis by Inhibiting Mitogen-activated Protein Kinase Pathway Activation and Phosphatidylethanolamine Externalization

The phosphatidylethanolamine (PE)-binding proteins (PEBPs) are an evolutionarily conserved family of proteins with pivotal biological functions. Here we describe the cloning and functional characterization of a novel family member, human phosphatidylethanolamine-binding protein 4 (hPEBP4). hPEBP4 is expressed in most human tissues and highly expressed in tumor cells. Its expression in tumor cells is further enhanced upon tumor necrosis factor (TNF) alpha treatment, whereas hPEBP4 normally co-localizes with lysosomes, TNFalpha stimulation triggers its transfer to the cell membrane, where it binds to Raf-1 and MEK1. L929 cells overexpressing hPEBP4 are resistant to both TNFalpha-induced ERK1/2, MEK1, and JNK activation and TNFalpha-mediated apoptosis. Co-precipitation and in vitro protein binding assay demonstrated that hPEBP4 interacts with Raf-1 and MEK1. A truncated form of hPEBP4, lacking the PE-binding domain, maintains lysosomal co-localization but has no effect on cellular responses to TNFalpha. Given that MCF-7 breast cancer cells expressed hPEBP4 at a high level, small interfering RNA was used to silence the expression of hPEBP4. We demonstrated that down-regulation of hPEBP4 expression sensitizes MCF-7 breast cancer cells to TNFalpha-induced apoptosis. hPEBP4 appears to promote cellular resistance to TNF-induced apoptosis by inhibiting activation of the Raf-1/MEK/ERK pathway, JNK, and PE externalization, and the conserved region of PE-binding domain appears to play a vital role in this biological activity of hPEBP4.

A lipid-specific toxin reveals heterogeneity of sphingomyelin-containing membranes

Little is known about the heterogenous organization of lipids in biological membranes. Sphingomyelin (SM) is a major plasma membrane lipid that forms lipid domains together with cholesterol and glycolipids. Using SM-specific toxin, lysenin, we showed that in cultured epithelial cells the accessibility of the toxin to SM is different between apical and basolateral membranes. Apical membranes are highly enriched with glycolipids. The inhibitory role of glycolipids in the binding of lysenin to SM was confirmed by comparing the glycolipid-deficient mutant melanoma cell line with its parent cell. Model membrane experiments indicated that glycolipid altered the local density of SM so that the affinity of the lipid for lysenin was decreased. Our results indicate that lysenin recognizes the heterogenous organization of SM in biomembranes and that the organization of SM differs between different cell types and between different membrane domains within the same cell. Isothermal titration calorimetry suggests that lysenin binding to SM is presumably the result of a SM-lysenin complex formation of specific stoichiometry, thus supporting the idea of the existence of small condensed lipid complexes consisting of just a few lipid molecules in living cells.

A survey of the year 2002 literature on applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is becoming widely accepted as a key instrument in any laboratory in which quantification of biomolecular interactions is a requisite. The method has matured with respect to general acceptance and application development over recent years. The number of publications on ITC has grown exponentially over the last 10 years, reflecting the general utility of the method. Here all the published works of the year 2002 in this area have been surveyed. We review the broad range of systems to which ITC is being directed and classify these into general areas highlighting key publications of interest. This provides an overview of what can be achieved using this method and what developments are likely to occur in the near future.

Cinnamycin (Ro 09-0198) promotes cell binding and toxicity by inducing transbilayer lipid movement

Cinnamycin is a unique toxin in that its receptor, phosphatidylethanolamine (PE), resides in the inner layer of the plasma membrane. Little is known about how the toxin recognizes PE and causes cytotoxicity. We showed that cinnamycin induced transbilayer phospholipid movement in target cells that leads to the exposure of inner leaflet PE to the toxin. Model membrane studies revealed that cinnamycin induced transbilayer lipid movement in a PE concentration-dependent manner. Re-orientation of phospholipids was accompanied by an increase in the incidence of beta-sheet structure in cinnamycin. When the surface concentration of PE was high, cinnamycin induced membrane re-organization such as membrane fusion and the alteration of membrane gross morphology. These results suggest that cinnamycin promotes its own binding to the cell and causes toxicity by inducing transbilayer lipid movement.