Nuclear magnetic resonance investigation of the conformation of delta-haemolysin bound to dodecylphosphocholine micelles

Legionella pneumophila: The Paradox of a Highly Sensitive Opportunistic Waterborne Pathogen Able to Persist in the Environment

Legionella pneumophila, the major causative agent of Legionnaires’ disease, is found in freshwater environments in close association with free-living amoebae and multispecies biofilms, leading to persistence, spread, biocide resistance, and elevated virulence of the bacterium. Indeed, legionellosis outbreaks are mainly due to the ability of this bacterium to colonize and persist in water facilities, despite harsh physical and chemical treatments. However, these treatments are not totally efficient and, after a lag period, L. pneumophila may be able to quickly re-colonize these systems. Several natural compounds (biosurfactants, antimicrobial peptides…) with anti-Legionella properties have recently been described in the literature, highlighting their specific activities against this pathogen. In this review, we first consider this hallmark of Legionella to resist killing, in regard to its biofilm or host-associated life style. Then, we focus more accurately on natural anti-Legionella molecules described so far, which could provide new eco-friendly and alternative ways to struggle against this important pathogen in plumbing.

Spatial structure of heptapeptide Aβ(16-22) (beta-amyloid Aβ(1-40) active fragment) in solution and in complex with a biological membrane model

The spatial structure of an active fragment of beta-amyloid Aβ(1-40) heptapeptide Aβ(16-22) (Lys-Leu-Val-Phe-Phe-Ala-Glu) in aqueous buffer solution and in complex with sodium dodecyl sulfate micelles as a model membrane system was investigated by (1)H NMR spectroscopy and two-dimensional NMR (TOCSY, HSQC-HECADE (Heteronuclear Couplings from ASSCI-domain experiments with E.COSY-type crosspeaks), NOESY) spectroscopy. Complex formation was confirmed by the chemical shift changes of the heptapeptide's (1)H NMR spectra, as well as by the signs and values of the NOE effects in different environments. We compared the spatial structure of the heptapeptide in borate buffer solution and in complex with a model of the cell surface membrane.

Inhibition of colony-spreading activity of Staphylococcus aureus by secretion of δ-hemolysin

Staphylococcus aureus spreads on the surface of soft agar, a phenomenon we termed "colony spreading." Here, we found that S. aureus culture supernatant inhibited colony spreading. We purified δ-hemolysin (Hld, δ-toxin), a major protein secreted from S. aureus, as a compound that inhibits colony spreading. The culture supernatants of hld-disrupted mutants had 30-fold lower colony-spreading inhibitory activity than those of the parent strain. Furthermore, hld-disrupted mutants had higher colony-spreading ability than the parent strain. These results suggest that S. aureus negatively regulates colony spreading by secreting δ-hemolysin.

NMR analysis of unnatural amino acids in natural antibiotics

A large number of modified amino acids other than the canonical amino acid residues can be found in natural products, especially antibiotics. The structure of these peptide-based compounds is investigated using modern two-dimensional NMR techniques. The automatic assignment of the 2D NMR proton spectra and consequent determination of the primary and 3D structure of peptides or small size proteins containing natural amino acids is nowadays routine. However, a deficiency in the ability to readily sequence peptides containing unnatural amino acids still remains and a great human effort and time is required. The experimental methods and the protocols of manual analysis of the data are described in the following sections.

Interaction of the antimicrobial peptide melimine with bacterial membranes

Melimine is a novel cationic peptide possessing broad-spectrum antimicrobial activity that is retained when attached to a surface, suggesting that interactions with bacterial membranes may be of primary importance to its activity. The effects of alterations in the environment on the conformation of melimine were investigated using circular dichroism and fluorescence spectra in membrane-mimetic solvents. Furthermore, the interactions of melimine with bacterial membranes of Pseudomonas aeruginosa and Staphylococcus aureus were examined using scanning electron and fluorescence microscopy, and perturbation of membrane integrity was tested by measurement of melimine-mediated diSC(3)-5 dye release from bacterial cells. Melimine has a predominantly random coil conformation that adopts a helical fold when exposed to organic solvents. However, when it is solubilised in micelles of sodium dodecyl sulphate, which are bacterial membrane-mimetic, the alpha-helical content increases to ca. 35-40%. A major effect of melimine was on the integrity of the cytoplasmic membrane both for P. aeruginosa and S. aureus. However, for P. aeruginosa the rapid loss of cytoplasmic membrane integrity correlated directly with loss of cell viability, whilst for S. aureus maximal dye release was obtained at concentrations where there was no significant loss of viability. There have been few studies to date investigating differences in the action of cationic peptides towards Gram-positive and Gram-negative bacteria. Consequently, further investigation of these mechanistic differences may allow more refined targeting of increasingly difficult-to-treat bacterial infections and/or further inform design of novel peptides with improved broad-spectrum activity.

Detergent-like activity and alpha-helical structure of warnericin RK, an anti-Legionella peptide

Warnericin RK is the first antimicrobial peptide known to be active against Legionella pneumophila, a pathogen bacterium that is responsible for severe pneumonia. Strikingly, this peptide displays a very narrow range of antimicrobial activity, almost limited to the Legionella genus, and a hemolytic activity. A similar activity has been described for delta-lysin, a well-known hemolytic peptide of Staphylococci that has not been described as antimicrobial. In this study we aimed to understand the mode of action of warnericin RK and to explain its particular target specificity. We found that warnericin RK permeabilizes artificial membranes in a voltage-independent manner. Osmotic protection experiments on erythrocytes showed that warnericin RK does not form well-defined pores, suggesting a detergent-like mode of action, as previously described for delta-lysin at high concentrations. Warnericin RK also permeabilized Legionella cells, and these cells displayed a high sensitivity to detergents. Depending on the detergent used, Legionella was from 10- to 1000-fold more sensitive than the other bacteria tested. Finally, the structure of warnericin RK was investigated by means of circular dichroism and NMR spectroscopy. The peptide adopted an amphiphilic alpha-helical structure, consistent with the proposed mode of action. We conclude that the specificity of warnericin RK toward Legionella results from both the detergent-like mode of action of the peptide and the high sensitivity of these bacteria to detergents.

Mechanisms of antimicrobial, cytolytic, and cell-penetrating peptides: from kinetics to thermodynamics

The mechanisms of six different antimicrobial, cytolytic, and cell-penetrating peptides, including some of their variants, are discussed and compared. The specificity of these polypeptides varies; however, they all form amphipathic alpha-helices when bound to membranes, and there are no striking differences in their sequences. We have examined the thermodynamics and kinetics of their interaction with phospholipid vesicles, namely, binding and peptide-induced dye efflux. The thermodynamics of binding calculated using the Wimley-White interfacial hydrophobicity scale are in good agreement with the values derived from experiment. The generally accepted view that binding affinity determines functional specificity is also supported by experiments in model membranes. We now propose the hypothesis that it is the thermodynamics of the insertion of the peptide into the membrane, from a surface-bound state, that determine the mechanism.

delta-hemolysin, an update on a membrane-interacting peptide

delta-hemolysin is a hemolytic peptide produced by Staphylococcus, and it has been studied for nearly 50 years. Therefore, it has become a model in the study of peptides interacting with membranes. In this review, we report some recent findings and compare them with previous works. delta-hemolysin is a 26 amino acid peptide, somewhat hydrophobic and presenting a zero net charge. Study of its structure has shown that delta-hemolysin is alpha-helical and amphipathic, such as many antimicrobial peptides (e.g. magainin and melittin). However, delta-hemolysin had not displayed any reported antimicrobial activity until a recent publication showed its high potency against Legionella. Its mode of action is based on direct interaction with target membranes. In accordance with its concentration, delta-hemolysin may slightly perturb a membrane or lead to cell lysis. Peptide charge plays an important role in its interaction with membranes, as is shown in the study of peptide variants. Some positively charged variants become highly hemolytic and even active against Escherichia coli and Staphylococcus aureus. Finally, it has recently been demonstrated that peptide preferentially binds to lipid-disordered domains. It has been postulated that as a result, enrichment in lipid-ordered domains might increase peptide concentration in lipid-disordered domains and thereby improve its activity.

The activity of the amphipathic peptide delta-lysin correlates with phospholipid acyl chain structure and bilayer elastic properties

Release of lipid vesicle content induced by the amphipathic peptide delta-lysin was investigated as a function of lipid acyl chain length and degree of unsaturation for a series of phosphatidylcholines. Dye efflux and peptide binding were examined for three homologous lipid series: di-monounsaturated, di-polyunsaturated, and asymmetric phosphatidylcholines, with one saturated and one monounsaturated acyl chain. Except for the third series, peptide activity correlated with the first moment of the lateral pressure profile, which is a function of lipid acyl chain structure. In vesicles composed of asymmetric phosphatidylcholines, peptide binding and dye efflux are enhanced compared to symmetric, unsaturated lipids with similar pressure profiles. We attribute this to the entropically more favorable interaction of delta-lysin with partially saturated phospholipids. We find that lipid acyl chain structure has a major impact on the activity of delta-lysin and is likely to be an important factor contributing to the target specificity of amphipathic peptides.

Characterization of anti-Legionella activity of warnericin RK and delta-lysin I from Staphylococcus warneri

Legionella pneumophila, the causative agent of Legionnaires' disease, is a waterborne bacteria. It can multiply in man-made water systems and infect people who inhale contaminated droplets. We have previously reported a Staphylococcus warneri strain that display an anti-Legionella activity. In this work, we characterized three anti-Legionella peptides that are produced by S. warneri. One peptide, warnericin RK, is original, while the two others are delta-lysin I and delta-lysin II, whose genes were previously described. Due to high sequence similarity of the two delta-lysins, further characterization was performed only on delta-lysin I. Warnericin RK and delta-lysin I displayed the same antibacterial spectrum, which is almost restricted to the Legionella genus. Also, both peptides have a hemolytic activity. These results led to the hypothesis that warnericin RK and delta-lysin I share a similar mode of action, and that Legionella should have a specific feature that may explain the high specificity of these antibacterial peptides.

Interaction of polysorbate 80 with erythropoietin: a case study in protein-surfactant interactions

PURPOSE

The cause of antibody positive pure red cell aplasia associated with the subcutaneous administration of EPREX to patients with chronic kidney failure has been determined to be due to the leaching of weakly adjuvant compounds from the uncoated rubber stoppers that were formerly used in prefilled syringes. Other researchers have suggested that polysorbate 80 micelles containing erythropoietin may be a causative factor. The purpose of this work was to repeat previously published studies in a more controlled manner and to define the precise nature of the interactions between polysorbate 80 and erythropoietin.

METHODS

The contents of EPREX prefilled syringes and laboratory-prepared, well-characterized formulations of EPREX were analyzed by size exclusion chromatography. Fractions were analyzed for the presence of erythropoietin by ELISA. EPREX formulations prepared with increasing amounts of polysorbate 80 were analyzed by light scattering.

RESULTS

Well-controlled chromatographic studies showed that when EPREX formulations containing no aggregate were analyzed by high-performance liquid chromatography, erythropoietin monomer could not be detected under the polysorbate 80 peak. Dimer and oligomers of erythropoietin coeluted under the polysorbate 80 peak as the molecular weights overlapped on the size exclusion chromatogram. Solution light scattering indicated that polysorbate 80 associates with erythropoietin in a defined stoichiometric ratio of 1:12.

CONCLUSIONS

Based on controlled studies, previous results suggesting that EPREX contains micelle-associated erythropoietin were incorrect. As with other surfactants and proteins, polysorbate 80 associates with erythropoietin in a defined stoichiometric ratio.

Conformation and activity of delta-lysin and its analogs

Delta-Lysin is a 26-residue hemolytic peptide secreted by Staphylococcus aureus. Unlike the bee venom peptide melittin, delta-lysin does not exhibit antibacterial activity. We have synthesized delta-lysin and several analogs wherein the N-terminal residues of the toxin were sequentially deleted. The toxin has three aspartic acids, four lysines and no prolines. Analogs were also generated in which all the aspartic acids were replaced with lysines. A proline residue was introduced in the native sequences as well as in the analogs where aspartic acids were replaced with lysines. We observed that 20- and 22-residue peptides corresponding to residues 7-26 and 5-26 of delta-lysin, respectively, had greater hemolytic activity than the parent peptide. These shorter peptides, unlike delta-lysin, did not self-associate to adopt alpha-helical conformation in water, at lytic concentrations. Introduction of proline or substitution of aspartic acids by lysines resulted in loss in propensity to adopt helical conformation in water. When proline was introduced in the peptides corresponding to the native toxin sequence, loss of hemolytic activity was observed. Substitution of all the aspartic acids with lysines resulted in enhanced hemolytic activity in all the analogs. However, when both proline and aspartic acid to lysine changes were made, only antibacterial activity was observed in the shorter peptides. Our investigations on delta-lysin and its analogs provide insights into the positioning of anionic, cationic residues and proline in determining hemolytic and antibacterial activities.

Structure and activity of D-Pro14 melittin

D-Pro14 melittin was synthesized to investigate the effect of increasing the angle of the bend in the hinge region between the helical segments of the molecule. Structural analysis by nuclear magnetic resonance indicated that, in methanol, the molecule consisted of two helices separated at Pro14, as in melittin. However, the two helices in D-Pro14 melittin were laterally displaced relative to each other by approximately 7 A, and in addition, there was a small rotation of the carboxyl-terminal helix relative to the amino-terminal helix around the long axis of the molecule. The peptide had less than 5% of the cytolytic activity of melittin. Modification of Arg22 with the 2,2,5,7,8-pentamethyl-chroman-6-sulphonyl (pmc) group restored hemolytic activity to close to that of unmodified melittin. Replacement of Arg22 with Phe was less effective in restoring hemolytic activity. Electron-paramagnetic resonance studies suggest that there is a positive correlation between hemolytic activity of the peptides and interaction with phospholipid bilayers.

Peptide hormone binding to G-protein-coupled receptors: structural characterization via NMR techniques

G-protein-coupled receptors (GPCRs) allow cells to respond to calcium, hormones, and neurotransmitters. Not surprisingly, they currently make up the largest family of validated drug targets. Rational drug design for molecular regulators targeting GPCRs has been limited to theoretical-based computational approaches. X-ray crystallography of intact GPCRs has provided the topological orientation of the seven transmembrane helices, but limited structural information of the extracellular and intracellular loops and protein termini. In this review we detail an NMR-based approach which provides the high-resolution structural features on the extracellular domains of GPCRs and the ligand/receptor complexes formed upon titration of the peptide hormone. The results provide important contact points and a high-resolution description of the ligand/receptor interactions, which may be useful for the rational design of therapeutic agents targeting GPCRs. Recent results from our investigation of the cholecystokinin peptide hormone system are used to highlight this approach.

Substance P (free acid) adopts different conformation than native peptide in DMSO, water and DPPC bilayers

The conformation of substance P (free acid) (SPOH) has been investigated in dimethylsulfoxide (DMSO), water and dipalmitoylphosphotidylcholine (DPPC) bilayers by two-dimensional NMR and restraint molecular dynamics simulations. The observed NOE patterns for SPOH in these media are very much different from each other. Molecular modeling of the conformation of SPOH by incorporating NOEs as distance restraints shows wide differences in its conformation in three media. The main structural features for SPOH in DMSO are y-bends at Pro4 and Phe7 along with a non-specific bend around Lys3-Pro4-Gln5-Gln6, which are stabilized by Lys3CO-->Gln5NH, Gln6CO-->Phe8NH hydrogen bonding. The more flexible conformation of SPOH in water is transformed to an ordered structure after incorporation in DPPC bilayers. The conformation of SPOH in DPPC bilayers is characterized by gamma-bends at Pro4, Gln6 and Phe7, which are stabilized by hydrogen bonding between Lys3CO-->Gln5NH, Gln5CO-->Phe7NH and Gln6CO-->Phe8NH, respectively. The absence of biological activity in SPOH has been attributed to the absence of any helix like structure at the central residues and absence of any interresidue interaction with C-terminal OH group, in DPPC bilayers, a feature shown to be an important prerequisite for SP and SP agonists to bind to the NKI tachykinin receptor.

Maculatin 1.1, an anti-microbial peptide from the Australian tree frog, Litoria genimaculata solution structure and biological activity

The dorsal glands of Australian tree frogs from the Litoria species contain a diversity of antibiotic peptides that forms part of the defence system of the animal. Here, the antibiotic activity and structure of maculatin 1.1, a 21 amino acid peptide from Litoria genimaculata, are compared. The activity data on maculatin 1.1 and a series of its analogues imply that the mechanism of action of maculatin 1.1 involves binding to, and subsequent lysis of, the bacterial cell membrane. The structure of maculatin 1.1 was determined using NMR spectroscopy in a trifluoroethanol/water mixture and when incorporated into dodecylphosphocholine micelles. Under both conditions, the peptide adopts a very similar conformation, i.e. a helical structure with a central kink in the vicinity of Pro15. The kink allows the peptide to adopt a well-defined amphipathic conformation along its entire length. The similar structures determined under both solvent conditions imply that structures of membrane-interacting peptides in trifluoroethanol/water mixtures are representative of those adopted in a membrane environment, e.g. when incorporated into micelles. The synthetic Ala15 analogue of maculatin 1.1 has markedly reduced activity and its NMR-derived structure is a well-defined helix, which lacks the central kink and flexibility of the parent molecule. It is concluded that the kink is important for full biological activity of the peptide, probably because it allows maximum amphipathicity of the peptide to facilitate interaction with the membrane. The structure of maculatin 1.1 is compared with a related peptide, caerin 1.1 [Wong, H., Bowie, J.H. and Carver, J.A. (1997) Eur. J. Biochem. 247, 545-557], which has an additional central proline residue and enhanced central flexibility compared with maculatin 1.1. The role of central flexibility within antibiotic peptides in their interaction with bacterial membranes is discussed.

Exotoxins of Staphylococcus aureus

This article reviews the literature regarding the structure and function of two types of exotoxins expressed by Staphylococcus aureus, pyrogenic toxin superantigens (PTSAgs) and hemolysins. The molecular basis of PTSAg toxicity is presented in the context of two diseases known to be caused by these exotoxins: toxic shock syndrome and staphylococcal food poisoning. The family of staphylococcal PTSAgs presently includes toxic shock syndrome toxin-1 (TSST-1) and most of the staphylococcal enterotoxins (SEs) (SEA, SEB, SEC, SED, SEE, SEG, and SEH). As the name implies, the PTSAgs are multifunctional proteins that invariably exhibit lethal activity, pyrogenicity, superantigenicity, and the capacity to induce lethal hypersensitivity to endotoxin. Other properties exhibited by one or more staphylococcal PTSAgs include emetic activity (SEs) and penetration across mucosal barriers (TSST-1). A detailed review of the molecular mechanisms underlying the toxicity of the staphylococcal hemolysins is also presented.

Exotoxins of Staphylococcus aureus

This article reviews the literature regarding the structure and function of two types of exotoxins expressed by Staphylococcus aureus, pyrogenic toxin superantigens (PTSAgs) and hemolysins. The molecular basis of PTSAg toxicity is presented in the context of two diseases known to be caused by these exotoxins: toxic shock syndrome and staphylococcal food poisoning. The family of staphylococcal PTSAgs presently includes toxic shock syndrome toxin-1 (TSST-1) and most of the staphylococcal enterotoxins (SEs) (SEA, SEB, SEC, SED, SEE, SEG, and SEH). As the name implies, the PTSAgs are multifunctional proteins that invariably exhibit lethal activity, pyrogenicity, superantigenicity, and the capacity to induce lethal hypersensitivity to endotoxin. Other properties exhibited by one or more staphylococcal PTSAgs include emetic activity (SEs) and penetration across mucosal barriers (TSST-1). A detailed review of the molecular mechanisms underlying the toxicity of the staphylococcal hemolysins is also presented.

Replacement of phe(8) in substance P by tyr (Tyr(8)-SP) alters the conformation of the peptide in DMSO, water, and lipid bilayers

The conformation of [Tyr(8)]SP (Y8SP) in dimethylsulfoxide (DMSO), water, and dipalmitoyl phosphatidylcholine (DPPC) bilayers has been investigated by two-dimensional nmr and molecular dynamics simulations. Molecular modeling of the conformation of Y8SP by incorporating nuclear Overhauser effects as distance restraints shows wide differences in its conformation in the three media. In DMSO, the main structural features are gamma-bends along with a nonspecific bend around Gln(6)-Phe(7)-Tyr(8). The random coil structure seen in water is transformed into a beta-turn around the segment Gln(5)-Gln(6)-Phe(7)-Tyr(8) when Y8SP is incorporated into DPPC bilayers. The lower biological activity of Y8SP compared to the native peptide (SP) has been attributed to the absence of any helix like structure at the central residues, a feature shown to be an important prerequisite for SP and SP agonists to bind to the neurokinin 1 tachykinin receptor.

Structural features of helical aggregates of antibacterial peptides via simulated annealing and molecular modeling

A 27-residue stretch of amino acids encompassing two putative 13-residue amphiphilic helical segments is an important determinant of activity in the 47-residue antibacterial peptide bovine seminalplasmin. Synthetic peptides corresponding to the 27-residue stretch (P27) SLSRYAKLANRLANPKLLETFLSKWIG as well as the 13-residue segments PKLLETFLSKWIG (SPF),exhibit antimicrobial activity. An analog of SPF where E has been replaced by K(SPFK) showed improved antimicrobial properties as compared to SPF. The peptides have the ability to bind and permeabilize membranes. We have modeled helical bundles of P27 and the two 13-residue peptides SPF and SPFK using simulated annealing via molecular dynamics. Octameric but not hexameric aggregates of P27 can form channels which would allow the passage of ions. In the case of 13-residue peptides, aggregates formed by 6 monomers can conceivably form ion conducting channels. Since the ability to form channels which would allow the passage of ions across the membranes is an important determinant of the biological activities of these peptides, knowledge of the pore forming structures should help in the design of analogs with improved activities.

Thermodynamic model of secondary structure for alpha-helical peptides and proteins

A thermodynamic model describing formation of alpha-helices by peptides and proteins in the absence of specific tertiary interactions has been developed. The model combines free energy terms defining alpha-helix stability in aqueous solution and terms describing immersion of every helix or fragment of coil into a micelle or a nonpolar droplet created by the rest of protein to calculate averaged or lowest energy partitioning of the peptide chain into helical and coil fragments. The alpha-helix energy in water was calculated with parameters derived from peptide substitution and protein engineering data and using estimates of nonpolar contact areas between side chains. The energy of nonspecific hydrophobic interactions was estimated considering each alpha-helix or fragment of coil as freely floating in the spherical micelle or droplet, and using water/cyclohexane (for micelles) or adjustable (for proteins) side-chain transfer energies. The model was verified for 96 and 36 peptides studied by 1H-nmr spectroscopy in aqueous solution and in the presence of micelles, respectively ([set 1] and [set 2]) and for 30 mostly alpha-helical globular proteins ([set 3]). For peptides, the experimental helix locations were identified from the published medium-range nuclear Overhauser effects detected by 1H-nmr spectroscopy. For sets 1, 2, and 3, respectively, 93, 100, and 97% of helices were identified with average errors in calculation of helix boundaries of 1.3, 2.0, and 4.1 residues per helix and an average percentage of correctly calculated helix-coil states of 93, 89, and 81%, respectively. Analysis of adjustable parameters of the model (the entropy and enthalpy of the helix-coil transition, the transfer energy of the helix backbone, and parameters of the bound coil), determined by minimization of the average helix boundary deviation for each set of peptides or proteins, demonstrates that, unlike micelles, the interior of the effective protein droplet has solubility characteristics different from that for cyclohexane, does not bind fragments of coil, and lacks interfacial area.

Solution conformations of peptides representing the sequence of the toxin pardaxin and analogues in trifluoroethanol-water mixtures: analysis of CD spectra

The cytolytic activities and conformational properties of pardaxin (GFFALIPKIISSPLFKTLLSAVGSALSSSGEQE), a 33-residue linear peptide that exhibits unusual shark repellent and cytolytic activities, and its analogues have been examined in aqueous environment and trifluoroethanol (TFE) using CD spectroscopy. A peptide corresponding to the 1-26 segment and an analogue where P7 has been changed to A show greater hemolytic activity than pardaxin. While the peptide corresponding to the N-terminal 18-residue segment does not exhibit hemolytic activity, its analogue where P7 is replaced by A is hemolytic. The secondary structural propensities of the peptides were inferred by deconvolution of the experimental spectra into pure components. Pardaxin, its variant where proline at position 7 was replaced by alanine, and shorter peptides corresponding to N-terminal segments exist in multiple conformations in aqueous medium that are comprised of beta-turn, beta-sheet, and distorted helical structures. With increasing proportions of TFE, while helical conformation predominates in all the peptides, both distorted and the regular alpha-helices appear to be populated. Analysis of CD spectra by deconvolution methods appears to be a powerful tool for delineating multiple conformations in peptides, especially membrane-active peptides that encounter media of different polarity ranging from aqueous environment to one of low dielectric constant in the hydrophobic interior of membranes. Our study provides further insights into the structural requirements for the biological activity of pardaxin and related peptides.

Simulation of voltage-dependent interactions of alpha-helical peptides with lipid bilayers

Pore formation in lipid bilayers by channel-forming peptides and toxins is thought to follow voltage-dependent insertion of amphipathic alpha-helices into lipid bilayers. We have developed an approximate potential for use within the CHARMm molecular mechanics program which enables one to simulate voltage-dependent interaction of such helices with a lipid bilayer. Two classes of helical peptides which interact with lipid bilayers have been studied: (a) delta-toxin, a 26 residue channel-forming peptide from Staphylococcus aureus; and (b) synthetic peptides corresponding to the alpha 5 and alpha 7 helices of the pore-forming domain of Bacillus thuringiensis CryIIIA delta-endotoxin. Analysis of delta-toxin molecular dynamics (MD) simulations suggested that the presence of a transbilayer voltage stabilized the inserted location of delta-toxin helices, but did not cause insertion per se. A series of simulations for the alpha 5 and alpha 7 peptides revealed dynamic switching of the alpha 5 helix between a membrane-associated and a membrane-inserted state in response to a transbilayer voltage. In contrast the alpha 7 helix did not exhibit such switching but instead retained a membrane associated state. These results are in agreement with recent experimental studies of the interactions of synthetic alpha 5 and alpha 7 peptides with lipid bilayers.

Peptide models for membrane channels

Peptides may be synthesized with sequences corresponding to putative transmembrane domains and/or pore-lining regions that are deduced from the primary structures of ion channel proteins. These can then be incorporated into lipid bilayer membranes for structural and functional studies. In addition to the ability to invoke ion channel activity, critical issues are the secondary structures adopted and the mode of assembly of these short transmembrane peptides in the reconstituted systems. The present review concentrates on results obtained with peptides from ligand-gated and voltage-gated ion channels, as well as proton-conducting channels. These are considered within the context of current molecular models and the limited data available on the structure of native ion channels and natural channel-forming peptides.

Ion channel formation by synthetic analogues of staphylococcal delta-toxin

Ion channel formation by three analogues of staphylococcal delta-toxin, an amphipathic and alpha-helical channel-forming peptide, has been evaluated by measurement of ionic currents across planar lipid bilayers. Replacement of beta-branched, hydrophobic residues by leucine and movement of a tryptophan residue from the hydrophilic to the hydrophobic face of the helix does not significantly alter ion channel activity. Removal of the N-terminal blocking group combined with the substitution of glycine-10 by leucine changes the single channel properties of delta-toxin, without altering macroscopic conductance/voltage behaviour. Truncation of the N-terminus by three residues results in complete loss of channel-forming activity. These changes in channel-forming properties upon altering the peptide sequence do not mirror changes in haemolytic activity. The results lend support to the proposal that channel formation and haemolysis are distinct events. Channel properties are discussed in the context of a model in which the pore is formed by a bundle of approximately parallel transbilayer helices.

Pulmonary surfactant-associated polypeptide SP-C in lipid micelles: CD studies of intact SP-C and NMR secondary structure determination of depalmitoyl-SP-C(1-17)

The surfactant-associated polypeptide C (SP-C) is a 35-residue lipopolypeptide which is essential for the function of surfactants used for therapy of infant respiratory distress. Modeling based on the recently determined nuclear magnetic resonance (NMR) structure of native SP-C in an organic solvent showed that SP-C could readily insert into fluid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayers. The present paper describes further physical-chemical studies of intact SP-C and its N-terminal 17-residue polypeptide fragment, depalmitoyl-SP-C(1-17), in the presence of dodecylphosphocholine micelles. The results obtained provide a link between the NMR solution structure and the behaviour of SP-C in an ordered lipid environment, and thus present new insights for rational design of SP-C analogs for therapeutic purposes.

Ether lipids in biomembranes

Plasmalogens (1-O-1'-alkenyl-2-acylglycerophospholipids) and to a lesser extent the 1-O-alkyl analogs are ubiquitous and in some cases major constituents of mammalian cellular membranes and of anaerobic bacteria. In archaebacteria polar lipids of the cell envelope are either diphytanylglycerolipids or bipolar macrocyclic tetraether lipids capable of forming covalently linked 'bilayers'. Information on the possible role of ether lipids as membrane constituents has been obtained from studies on the biophysical properties of model membranes consisting of these lipids. In addition, effects of modified ether lipid content on properties of biological membranes have been investigated using microorganisms or mammalian cells which carry genetic defects in ether lipid biosynthesis. Differential utilization of ether glycerophospholipids by specific phospholipases might play a role in the generation of lipid mediators that are involved in signal transduction. A possible function of plasmalogens as antioxidants has been demonstrated with cultured cells and might play a role in serum lipoproteins. Synthetic ether lipid analogs exert cytostatic effects, most likely by interfering with membrane structure and by specific interaction with components of signal transmission pathways, such as phospholipase C and protein kinase C.

Cell-lytic and antibacterial peptides that act by perturbing the barrier function of membranes: facets of their conformational features, structure-function correlations and membrane-perturbing abilities

Almost all hemolytic and antimicrobial peptides form part of the defense mechanism of species widely distributed across the evolutionary scale. Although these peptides are of varying lengths and composition, they form amphiphilic structures in a hydrophobic environment. They also have the ability to form channels in natural and model membranes. Hemolytic peptides have proven to be very useful in studying the mechanism of hemolysis and the permeability properties of red blood cells. Preliminary investigations indicate that these peptides may also be useful in the investigation of complex cellular phenomena like exocytosis and neurotransmission. Although molecules like vancomycin, bacitracin and penicillins have been extensively used as antibiotics for therapeutic purposes, most species throughout the evolutionary scale use peptides as antimicrobial agents. These peptides exert their activity by altering the permeability properties of the bacterial plasma membrane and do not interfere with macro molecular synthesis like the other antibiotics that are presently used in therapies. Hence it is likely that resistance to peptide antibacterial agents may not develop easily. Since the problem of antibiotic resistance is presently a particularly severe one, peptide antibiotics may be the drugs of choice in the future.

Seminal plasmin, a bovine seminal plasma protein, lyses dividing but not resting mammalian cells

Seminal plasmin, an antimicrobial and transcription-inhibitory protein of bovine seminal plasma, is shown to lyse dividing mammalian cells in vitro. It lyses cells in culture such as CHO, Vero, HeLa and L929. It also lyses regenerating rat liver parenchymal cells and cells of two ascitic tumours of rat--the Zajdela ascitic hepatoma and the AK-5. However, it does not lyse resting cells such as adult liver parenchymal cells, erythrocytes, or resting lymphocytes, though it binds to their cell surface. It can be used, therefore, to distinguish cells that are in the division cycle from cells that are in the resting phase. The cell-lytic activity of seminal plasmin is inhibited by Ca2+.

Methods to study membrane protein structure in solution

Membrane protein structure is difficult to determine by any technique. NMR spectroscopy of membrane proteins in solution can proceed using methods identical to those that have been successfully applied to numerous water-soluble proteins providing suitable solubilization conditions can be found. Organic solvents and small detergent micelles have correlation times short enough for structure determination based on 1H NOEs. Although it is difficult to generalize as each system is unique, organic solvents and micelles of strong detergents such as SDS are useful for amphiphilic peptides and small membrane proteins, whereas larger proteins need milder treatment to preserve the tertiary structure. Small unilamellar phospholipid vesicles are much too large for NOE-based structure determination, but they still fall under the domain of solution-state NMR and can be useful in certain circumstances.

Solution conformation of an antibacterial peptide, sarcotoxin IA, as determined by 1H-NMR

The solution conformation of sarcotoxin IA, which is an antibacterial peptide isolated from Sarcophaga peregrina with a molecular mass of 4 kDa, was determined by NMR spectroscopy and hybrid distance geometry/dynamical simulated annealing calculations. On the basis of 227 experimental constraints, including 185 distance constraints obtained from NOE and 42 constraints associated with 21 hydrogen bonds, a total of 18 converged structures of sarcotoxin IA were obtained. The final 18 converged structures exhibit backbone-atomic root-mean-square differences about the averaged coordinate positions of 0.070 +/- 0.027 nm for residues 3-23 and 0.040 +/- 0.017 nm for residues 28-38. It has been indicated that sarcotoxin IA consists of two amphiphilic alpha-helical regions, i.e. helix I (Leu3-Gln23) and helix II (Ala28-Ala38), with a hinge region (Gly24-Ile27), which connects helix I and helix II. We conclude that these two amphiphilic helical segments of sarcotoxin IA are of importance for the expression of the antibacterial activity.

Hydrophilic surface maps of channel-forming peptides: analysis of amphipathic helices

Ion channels may be formed by bundles of amphipathic alpha-helices aligned parallel to one another and spanning a lipid bilayer membrane, with the hydrophilic faces of the helices lining a central pore. In order to provide insight into the packing of such helices in bundles, a method has been developed to evaluate hydrophilic surface maps of amphipathic alpha-helices and to display these surfaces in a readily interpretable form. The procedure is based upon empirical energy calculations of interactions of a water molecule with an amphipathic alpha-helix. The method has been applied to three channel-forming peptides: Staphylococcal delta-toxin; alamethicin; and a synthetic leucine- and serine-containing peptide. Particular emphasis is placed upon the effects of sidechain conformational flexibility on hydrophilic surface maps. A family of models of the delta-toxin helix is generated by a simulated annealing procedure. The results of hydrophilic surface map analyses provide more exact definition of the centre of the hydrophilic face of amphipathic helices, and of the variation of the position of the centre in response to changes in sidechain conformation. This information is used to define families of preliminary models for a given ion channel, as is illustrated for delta-toxin.

Influence of staphylococcal delta-toxin on the phosphatidylcholine headgroup as observed using 2H-NMR

The interaction of the 8-toxin peptide isolated from Staphylococcus aureus with the headgroup region of lipid bilayer membranes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) was investigated using deuterium (2H) and phosphorus (31P) nuclear magnetic resonance (NMR) spectroscopy. At relatively low peptide/lipid ratios (P/L < 0.10), all 2H- and 31P-NMR spectral lineshapes at 25 degrees C were indicative of a single population of liquid-crystalline lipids in a bilayer arrangement. At these P/L ratios, delta-toxin had only marginal effects on the size of the quadrupole splitting measured from POPC labelled at either the alpha-methylene (POPC-alpha-d2) or the beta-methylene segment (POPC-beta-d2) of the choline headgroup and, similarly small effects on the magnitude of the chemical shift anisotropy (CSA) of the 31P-NMR spectrum. With increasing amounts of delta-toxin (0.10 < P/L < 0.15) the size of the 2H quadrupole splitting from POPC-alpha-d2, as well as the magnitude of the 31P-CSA, decreased progressively and rapidly. The quadrupole splitting from POPC-beta-d2, however, remained relatively unaffected. At yet higher levels of delta-toxin (P/L > 0.15), all 2H- and 31P-NMR spectra indicated the presence of multiple lipid populations experiencing varying degrees of increased conformational disordering. The spectral lineshapes of these apparently nonbilayer spectral components reverted to bilayer-type lineshapes upon lowering the measuring temperature to 5 degrees C. At the utmost highest level of delta-toxin measured here (P/L = 0.20), all 2H- and 31P-NMR spectra consisted of a single, broad, apparently nonbilayer-type component, indicative of hindered but virtual isotropic motional averaging of the POPC headgroups. In this case no reversion to bilayer-type spectra could be obtained by decreasing the temperature. We could obtain no evidence that the conformation of the choline headgroup of POPC was responding to any specific influence of delta-toxin on bilayer surface electrostatics.

Ion channels formed by amphipathic helical peptides. A molecular modelling study

Channel forming peptides (CFPs) are amphipathic peptides, of length ca. 20 residues, which adopt an alpha-helical conformation in the presence of lipid bilayers and form ion channels with electrophysiological properties comparable to those of ion channel proteins. We have modelled CFP channels as bundles of parallel trans-bilayer helices surrounding a central ion-permeable pore. Ion-channel interactions have been explored via accessible surface area calculations, and via evaluation of changes in van der Waals and electrostatic energies as a K+ ion is translated along the length of the pore. Two CFPs have been modelled: (a) zervamicin-A1-16, a synthetic apolar peptaibol related to alamethicin, and (b) delta-toxin from Staphylococcus aureus. Both of these CFPs have previously been shown to form ion channels in planar lipid bilayers, and have been shown to have predominantly helical conformations. Zervamicin-A1-16 channels were modelled as bundles of 4 to 8 parallel helices. Two related helix bundle geometries were explored. K(+)-channel interactions have been shown to involve exposed backbone carbonyl oxygen atoms. delta-Toxin channels were modelled as bundles of 6 parallel helices. Residues Q3, D11 and D18 generate favourable K(+)-channel interactions. Rotation of W15 about its C beta-C gamma bond has been shown to be capable of occluding the central pore, and is discussed as a possible model for sidechain conformational changes in relation to ion channel gating.

Conformations of neurotensin in solution and in membrane environments studied by 2-D NMR spectroscopy

Two-dimensional HOHAHA and ROESY nuclear magnetic resonance techniques are used to obtain complete proton resonance assignments and to perform a conformational investigation of the neuropeptide neurotensin (pGlu-Leu-Tyr-Glu-Asn-Lys-Pro-Arg-Arg-Pro-Tyr-Ile-Leu) in aqueous solution, methanol, and membrane-mimetic [deuterated sodium dodecylsulfate (SDS)] environments. Results suggest the absence of discernible elements of secondary structure in water and methanol. ROESY spectra confirm that Lys-Pro and Arg-Pro peptide bonds are all-trans, but that a significant population of cis Arg-Pro bonds arises in aqueous solution, which increases in the environment of SDS micelles. The conformational ensemble of the peptide is observed to narrow as it becomes bound through its cationic mid-region to SDS micelles, with the accompanying advent of local extended structure. The overall results indicate the inherent conformational flexibility of neurotensin, and emphasize the environmental dependence of conformation in peptides of medium length.

Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization

Defensins (molecular weight 3500 to 4000) act in the mammalian immune response by permeabilizing the plasma membranes of a broad spectrum of target organisms, including bacteria, fungi, and enveloped viruses. The high-resolution crystal structure of defensin HNP-3 (1.9 angstrom resolution, R factor 0.19) reveals a dimeric beta sheet that has an architecture very different from other lytic peptides. The dimeric assembly suggests mechanisms by which defensins might bind to and permeabilize the lipid bilayer.

Magnetic resonance of membranes

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The amphiphilic alpha-helix concept. Consequences on the structure of staphylococcal delta-toxin in solution and bound to lipids

Staphylococcal delta-toxin, a synthetic analogue and a fragment were studied in order to determine their structure in solution and bound in lipids. In solution, a self-association process is observed. Analytical ultracentrifuge and quasi-elastic light-scattering experiments suggest an isodesmic aggregation in the high concentration domain above 2 microM up to very large asymmetrical species. Decreasing concentrations below 2 microM of delta-toxin and the analogue allows dissociation, probably into monomers. The self-associated species are essentially alpha-helical (70%) with buried and highly immobilized Trp either at position 15 for natural delta-toxin or 16 for the analogue. At the lowest concentration studied, the alpha-helix content severely decreases down to 35% while Trp fluorescence shows that these residues are exposed to buffer. The fragment 11-26 is always monomeric and structureless. From all the data, a structural model of aggregated species is proposed with stacked antiparallel amphipathic rods. When bound to lipids, whatever their initial structure in solution, 26-residue long peptides mainly adopt an alpha-helix conformation (80%) while fragment 11-26 exhibits about 50% alpha-helix. The lipid-peptide interactions were quantitatively analysed. For fragment 11-26, a single-step mechanism fits the spectroscopic changes and defines a single monomeric bound structure. On the other hand, for the 26-residue-long analogue, multiple-step processes must occur. The data were analysed with a partition of tetramers into lipids followed by a partial dissociation. Finally, the affinity of fragment 11-26 severely decreases from micelles to fluid and gel-state bilayers. The partition coefficient of the delta-toxin analogue is higher than those of other more apolar peptides, such as melittin and alamethicin, correlating with Eisenberg's hydrophobic moments. It is therefore proposed that delta-toxin probably lies parallel to the surface, only penetrating weakly in lipids, depending on their packing.

Solubility as a function of protein structure and solvent components

This review deals with ways of stabilizing proteins against aggregation and with methods to determine, predict, and increase solubility. Solvent additives (osmolytes) that stabilize proteins are listed with a description of their effects on proteins and on the solvation properties of water. Special attention is given to areas where solubility limitations pose major problems, as in the preparation of highly concentrated solutions of recombinant proteins for structural determination with NMR and X-ray crystallography, refolding of inclusion body proteins, studies of membrane protein dynamics, and in the formulation of proteins for pharmaceutical use. Structural factors relating to solubility and possibilities for protein engineering are analyzed.

Structure and dynamics in proteins of pharmacological interest

This paper begins with a brief survey of the standard nuclear magnetic resonance (NMR) method for protein structure determination in solution, which has been applied successfully with numerous globular proteins with molecular weights in the range from 3,000 to 15,000. The results obtained show that for the core of globular proteins, the quality of the structures determined in solution can be comparable to that achieved with diffraction techniques using protein single crystals. In addition, they also indicate that a complete description of proteins in solution may include short-lived, transient structural features that could be of crucial importance for the functional properties. Several supplementary NMR techniques capable of characterizing diverse aspects of flexible polypeptide chains are discussed.

Delta-haemolysin from Staphylococcus aureus and model membranes. A solid-state 2H-NMR and 31P-NMR study

Solid-state 2H NMR and 31P NMR of 2H-enriched chains and polar head groups, respectively, of dipalmitoylglycerophosphatidylcholine/water dispersions were undertaken to investigate the action of delta-haemolysin from Staphylococcus aureus on biomembranes. When the lipid/toxin molar ratio, Ri, is greater than or equal to 10, the gel-phase 2H powder patterns and the temperature of the gel-fluid phase transition, tc, are unchanged by the presence of the toxin whereas the 31P powder spectra of polar head groups are perturbed. At t greater than tc, a detailed analysis of methylene ordering indicates that delta-haemolysin orders the lipid chains near tc and disorders them for t much greater than tc. These findings are interpreted in terms of peptide location with regard to the membrane and suggest that the position of the toxin depends on the temperature relative to tc. Experiments carried out at Ri = 4 exhibit sharp, isotropic 2H-NMR lines, at t greater than tc, indicating that delta-haemolysin promotes the appearance of very small objects undergoing fast isotropic reorientation which average to zero the quadrupolar interaction. Below tc, one observes gel-phase powder patterns which indicate that the bacterial toxin is unable to form such small structures with ordered dipalmitoylglycerophosphocholine phospholipids. From comparison of the action of delta-haemolysin with that of melittin on same lipids [Dufourc et al. (1986) Biochemistry 25, 6448-6455] it results that both toxins perturb similarly fluid-phase lipids at elevated temperature, but they behave differently with gel-phase lipids, the former toxin being less efficient in membrane restructuring than the latter.