Mass spectrometric determination of molecular formulas for membrane-modifying antibiotics

Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study

Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature.

Hypersensitive-like response to the pore-former peptaibol alamethicin in Arabidopsis thaliana

In Arabidopsis thaliana cell cultures, the peptaibol alamethicin induced a form of active cell death that was associated with cell shrinkage and DNA fragmentation. The transfer of mature A. thaliana plants from a peptide-free medium to a medium containing a moderate concentration of alamethicin caused the development of lesions in leaves after a few days. These lesions were characterized by cell death, deposition of callose, production of autofluorescent phenolic compounds, and transcription of defense genes, just like in the hypersensitive response to a pathogen attack. The induction of defense-like responses in Arabidopsis by other membrane-disrupting peptides was also evaluated. The peptides selected for comparison included the natural antimicrobial melittin and the peptaibol ampullosporin A, as well as synthetic analogues of the peptaibols cervinin and trichogin. The response amplitude in A. thaliana increased with the peptaibol's ability to permeabilize biological membranes through a pore-forming mechanism and was strongly associated with their content in the helicogenic α-aminoisobutyric acid residue.

Plasma membrane-porating domain in poliovirus 2B protein. A short peptide mimics viroporin activity

Picornavirus 2B, a non-structural protein required for effective viral replication, has been implicated in cell membrane permeabilization during the late phases of infection. Here, we have approached the molecular mechanism of this process by assessing the pore-forming activity of an overlapping peptide library that spanned the complete 2B sequence. At non-cytopathic concentrations, only the P3 peptide, spanning 2B residues 35-55, effectively assembled hydrophilic pores that allowed diffusion of low molecular mass solutes across the cell plasma membrane (IC(50) approximately 4x10(-7) M) and boundary liposome bilayers (starting at peptide to lipid molar ratios>1:10(4)). Circular dichroism data were consistent with its capacity to fold as a helix in a membrane-like environment. Furthermore, addition of this peptide to a sealed plasma-membrane model, consisting of retinal rod outer segments patch-clamped in a whole-cell configuration, induced ion channel activity within seconds at concentrations as low as 10(-8) M. Thus, we have established a "one-helix" 2B version that possesses the intrinsic pore-forming activity required to directly and effectively permeabilize the cell plasma membrane. We conclude that 2B viroporin can be classified as a genuine pore-forming toxin of viral origin, which is produced intracellularly at certain times post infection.

Peptaibols and related peptaibiotics of Trichoderma. A review

Peptaibols and the related peptaibiotics are linear, amphipathic polypeptides. More than 300 of these secondary metabolites have been described to date. These compounds are composed of 5-20 amino acids and are generally produced in microheterogeneous mixtures. Peptaibols and peptaibiotics with unusual amino acid content are the result of non-ribosomal biosynthesis. Large multifunctional enzymes known as peptide synthetases assemble these molecules by the multiple carrier thiotemplate mechanism from a remarkable range of precursors, which can be N-methylated, acylated or reduced. Peptaibols and peptaibiotics show interesting physico-chemical and biological properties including the formation of pores in bilayer lipid membranes, as well as antibacterial, antifungal, occasionally antiviral activities, and may elicit plant resistance. The three-dimensional structure of peptaibols and peptaibiotics is characterized predominantly by one type of the helical motifs alpha-helix, 3(10)-helix and beta-bend ribbon spiral. The aim of this review is to summarize the data available about the biosynthesis, biological activity and conformational properties of peptaibols and peptaibiotics described from Trichoderma species.

Conversion of Ca2+ Salt of an Organic Compound to Its Li+ Salt to Simplify the Fast Atom Bombardment Mass Spectrum

The FAB mass spectrum of the Ca(2+) salt of RK-682 (1, MW 368), a potent protein tyrosine phosphatase inhibitor, shows a complex pattern due to Ca(2+) adduct ions with multimers of 1 and their decomposition ions. Addition of LiCl greatly simplified the FAB mass spectrum, providing a prominent Li(+) adduct ion of 1 at m/z 381 [M+2Li-H](+). The addition of LiCl also greatly simplified the FAB mass spectrum of calcium pantothenate. This approach may be generally useful for molecular weight determination of multivalent metal salts of organic compounds, or organic compounds that can form Li salts, by FAB mass spectrometry.

Molecular dynamics simulation of conformational flexibility of alamethicin fragments in aqueous and membranous environment

We present here results on molecular dynamics (MD) simulation on two fragments of channel forming antibiotic peptide Alamethicin, containing isoamino butyric acid (Aib). Simulations are carried out in aqueous and membranous environment in a bilayer of 39 molecules of Dimyristoyl phosphatidyl choline (DMPC). The peptides Boc-Pro-Aib-Ala-Aib-OBzl (Alam 1) and Boc-Leu-Aib-Pro-OBzl (Alam 2) were simulated from their crystallographic coordinates. The bilayers were built from two different conformations (A and B) of DMPC reported in crystal data. The P-N dipoles were arranged hexagonally with surface area per lipid molecule 66.5 A degrees 2 and P-P separation across the bilayer 34 A degrees. They were hydrated by 28.6 and 25.5 water molecules per DMPC molecule. Simulations are done using AMBER 4.0 package in constant number volume temperature (NVT) condition for 100 pico seconds (ps) in aqueous environment and 250 ps of equilibrated bilayer. Geometric parameters of lipids as: bilayer thickness, order parameter of the chains, transfraction of chain torsional angles were monitored. We also monitored geometric parameters of the peptides as backbone torsional angles, distances amongst C alpha atoms, angles between C alpha atoms, movement of center of gravity (CG) along and perpendicular to bilayer normal. We find that membrane bilayer is slightly disturbed due to the presence of peptides. In case of alam 2 in water angles phi 1 and phi 3 showed larger variation in water compared to same in the bilayer. The peptide conformation is more stable in DMPC bilayer. However the peptides showed movement along and perpendicular to bilayer normal. This we believe is due to hydrophobic nature of these peptides.

Preparation of site-specific isotopically labelled zervamicins, the antibiotic peptaibols produced by Emericellopsis salmosynnemata

A simple procedure for the preparation of the specifically labelled peptide antibiotic zervamicins IC, IIA and IIB has been developed. The zervamicin molecules are labelled with stable isotopes by culturing the Emericellopsis salmosynnemata on a well-defined synthetic medium containing the highly isotopically enriched amino acid. To obtain the peptide with the specifically and highly enriched amino acid residue, precautions have been taken to prevent any de novo biosynthesis of the particular amino acid from unlabelled precursors. The enrichment of the labelled peptide is determined by mass spectrometric analysis. Following this method we have incorporated [2',4',5',6',7'-2H5]-L-Trp-1, [1'-15N]-L-Trp-1 and [2',3',4',5',6'-2H5]-L-Phl-16 into zervamicins IC, IIA and IIB on the preparative scale and without scrambling of the label. Thus, using the procedures described, isotopically labelled zervamicins can be prepared, allowing them to be studied by solid-state NMR.

Two classes of alamethicin transmembrane channels: molecular models from single-channel properties

Molecular structures of transmembrane channels formed by alamethicin polypeptide aggregates were analyzed by measuring open-channel conductances and state-transition kinetics using voltage-clamp technique with artificial phospholipid bilayers isolated onto micropipettes by a novel solvent-free tip-dip method. Two distinct classes of alamethicin channels, each with a unique set of conductance states and kinetic properties, were identified. Alamethicin Rf50 at low temperatures forms mostly nonpersistent channels with lifetimes of < 1 min. Long-lasting persistent channels are formed by alamethicin Rf30 at all temperatures and by alamethicin Rf50 at room temperature. In the "modified barrel-stave" model for persistent channels based on the crystalline alamethicin secondary structure, the aqueous pore of the channel surrounded by parallel alamethicin monomers has a constriction generated by amino acid side chains protruding from the alamethicin helices into the pore. The model explains quantitatively the nonohmic channel conductance at high applied voltages and the conductance values and ion selectivities of various persistent channel states. The kinetic properties of nonpersistent channels are explained qualitatively by the "reversed-molecule" model in which nonpersistent channels differ from persistent channels by having one of the channel-forming alamethicin monomers oriented antiparallel to the others.

Molecular dynamics of alamethicin transmembrane channels from open-channel current noise analysis

Conductance noise measurement of the open states of alamethicin transmembrane channels reveals excess noise attributable to cooperative low-frequency molecular dynamics that can generate fluctuations approximately 1 A rms in the effective channel pore radius. Single-channel currents through both persistent and nonpersistent channels with multiple conductance states formed by purified polypeptide alamethicin in artificial phospholipid bilayers isolated onto micropipettes with gigaohm seals were recorded using a voltage-clamp technique with low background noise (rms noise < 3 pA up to 20 kHz). Current noise power spectra between 100 Hz and 20 kHz of each open channel state showed little frequency dependence. Noise from undetected conductance state transitions was insignificant. Johnson and shot noises were evaluated. Current noise caused by electrolyte concentration fluctuation via diffusion was isolated by its dependence on buffer concentration. After removing these contributions, significant current noise remains in all persistent channel states and increases in higher conductance states. In nonpersistent channels, remaining noise occurs primarily in the lowest two states. These fluctuations of channel conductance are attributed to thermal oscillations of the channel molecular conformation and are modeled as a Langevin translational oscillation of alamethicin molecules moving radially from the channel pore, damped mostly by lipid bilayer viscosity.

Motionally restricted tryptophan environments at the peptide-lipid interface of gramicidin channels

The tryptophans in the gramicidin channel play a crucial role in the organization and function of the channel. The localization and dynamics of these tryptophans have been studied using fluorescence spectroscopy, especially utilizing environment-induced effects on the rates of solvent relaxation around these residues in membranes. When incorporated into model membranes of dioleoyl-sn-glycero-3-phosphocholine (DOPC), the tryptophans in the gramicidin channel exhibit a red edge excitation shift (REES) of 6 nm. In addition, fluorescence polarization shows both excitation and emission wavelength dependence. Fluorescence lifetime analysis shows a biexponential decay, corresponding to a short- and a long-lifetime component. The mean lifetime was found to be dependent on both excitation and emission wavelengths. Analysis of time-resolved emission spectra (TRES) shows a heterogeneous environment for the tryptophans consistent with the lifetime information. Taken together, these observations point out the motional restriction experienced by the tryptophans in the gramicidin channel. This is consistent with other studies in which such restrictions are thought to be imposed due to hydrogen bonding between the indole rings of the tryptophans and the neighboring lipid carbonyls. The significance of such organization in terms of functioning of the channel is brought out by the fact that substitution, photodamage, or chemical modification of these tryptophans is known to give rise to channels with conformation and reduced conductivity.

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.

Incorporation kinetics in a membrane, studied with the pore-forming peptide alamethicin

The reaction of fluorescence-labeled alamethicin with unilamellar phospholipid vesicles (DOPC and DMPC) has been investigated in a stopped-flow apparatus. Clearly single exponential time functions have been observed at temperatures above the phase transition of the bilayer. This can be interpreted in terms of an essentially one-step incorporation process. The pseudo first-order forward rate is found to be quite fast, falling in a range somewhat below the diffusion controlled upper bound. The data are quantitatively very well described on the basis of a simple mechanism. This comprises diffusion of peptide into the bilayer accompanied by a more or less slower change of the secondary structure. Aggregation of the incorporated molecules at higher concentrations is indicated to be comparatively rapid.

Fast atom bombardment mass spectrometry and its application to the analysis of some peptides and proteins

The techniques of fast atom bombardment mass spectrometry has overtaken (but not entirely replaced) field desorption mass spectrometry as the method of choice for the analysis of nonvolatile, thermally labile polar compounds. The ease with which information may be obtained on a wide variety of molecules is a result of the relative simplicity of the technique. A brief history of bioorganic mass spectrometry leading to the development of fast atom bombardment is presented, as well as a description of the method and ancillary techniques. Selected examples of its application to peptide and protein structural problems attest to the power and utility of fast atom bombardment mass spectrometry.

Voltage-dependent channel formation by rods of helical polypeptides

The voltage-dependence of channel formation by alamethicin and it natural analogues can be described by a dipole flip-flop gating model, based on electric field-induced transbilayer orientational movements of single molecules. These field-induced changes in orientation result from the large permanent dipole moment of alamethicin, which adopts alpha-helical conformation in hydrophobic medium. It was, therefore, supposed that the only structural requirement for voltage-dependent formation of alamethicin-type channels might be a rigid lipophilic helical segment of minimum length. In order to test this hypothesis we synthesized a family of lipophilic polypeptides--Boc-(Ala-Aib-Ala-Aib-Ala)n-OMe, n = 1-4--which adopt alpha-helical conformation for n = 2-4 and studied their interaction with planar lipid bilayers. Surprisingly, despite their large difference in chain length, all four polypeptides showed quantitatively similar behavior. At low field strength of the membrane electric field these polypeptides induce a significant, almost voltage-independent increase of the bilayer conductivity. At high field strength, however, a strongly voltage-dependent conductance increase occurs similar to that observed with alamethicin. It results from the opening of a multitude of ion translocating channels within the membrane phase. The steady-state voltage-dependent conductance depends on the 8th-9th power of polypeptide concentration and involves the transfer of 4-5 formal elementary charges. From the power dependences on polypeptide concentration and applied voltage of the time constants in voltage-jump current-relaxation experiments, it is concluded that channels could be formed from preexisting dodecamer aggregates by the simultaneous reorientation of six formal elementary charges. Channels exhibit large conductance values of several nS, which become larger towards shorter polypeptide chain length. A mean channel diameter of 19 A is estimated corresponding roughly to the lumen diameter of a barrel comprised of 10 alpha-helical staves. Similar to experiments with the N-terminal Boc-derivative of alamethicin we did not observe the burst sequence of nonintegral conductance steps typical of natural (N-terminal Ac-Aib)-alamethicin. Saturation in current/voltage curves as well as current inactivation in voltage-jump current-relaxation experiments are found. This may be understood by assuming that channels are generated as dodecamers but, while reaching the steady state, reduce their size to that of an octamer or nonamer. We conclude that the overall behavior of these synthetic polypeptides is very similar to that of alamethicin.(ABSTRACT TRUNCATED AT 400 WORDS)

High field NMR study of antibiotic peptides: 1H assignment of trichorzianine A1 spectra by 2D experiments

A new antibiotic peptide, trichorzianine A1, was isolated from a culture of Trichoderma harzianum. It contains 19 residues, the N terminus is blocked by an acetyl group and the C terminus is tryptophanol. As a first part of the structural study of this new peptide, we here present the analysis of the 1H NMR spectrum accomplished by 2 DJ resolved and spin echo correlated spectroscopy.

Fast Atom Bombardment Mass Spectrometry

Fast atom bombardment mass spectrometry has become a powerful structural tool since the first reports of its use in 1981. Samples are ionized in the condensed state, usually in a glycerol matrix, by bombarding the matrix with xenon or argon atoms with energies of 5000 to 10,000 electron volts. This yields both positive and negative secondary ions, which are sputtered from the surface. The technique has been used to detect inorganic ion clusters to mass 25,800 and biologically active peptides to mass 5700, and it gives molecular ions of such highly polar or labile organic compounds as glycosphingolipids and polyene antibiotics. It can be especially valuable in determining the sequences of amino acids in polypeptides.

Identification and quantitation of methotrexate and methotrexate metabolites in clinical high-dose therapy by high pressure liquid chromatography and field desorption mass spectrometry

High-pressure liquid chromatography in combination with field desorption mass spectrometry as techniques of high specificity and sensitivity have been applied to the identification and quantitation of the anticancer drug methotrexate and its metabolites which occur in clinical high-dose therapy. Field desorption mass spectra of methotrexate and several methotrexate and folic acid derivatives, when investigated as free acids or ammonium salts, yield abundant protonated molecular ions and a consistent pattern of structurally significant fragments. High-pressure liquid chromatographic separation of methotrexate metabolites was performed on reverse-phase, C-18 columns using a volatile, ammonium bicarbonate/acetate containing mobile phase that was especially suited for the field desorption mass spectral analysis of isolated metabolites, and provided the definite identification of 7-hydroxymethotrexate and 4-[[2,4-diamino-6-pteridinyl]methyl]methylamino]-benzoic acid in serum and urine of patients treated with high-dose methotrexate. The high intensity and stability of the [MH]+ ions was found suitable for the quantitation of methotrexate and related folate analogues by field desorption mass spectrometry. A synthetic methotrexate derivative, methotrexate-gamma-(2-hydroxy)ethyl-amide was used as internal standard for the quantitative determination of methotrexate in serum and urine. In a study to comparatively assess the potential of specific quantitation methods, serum and urine levels of methotrexate and its major metabolite, 7-hydroxymethotrexate were determined by (i) an enzyme immunoassay, (ii) reverse phase high-pressure liquid chromatography and (iii) field desorption mass spectrometry. Results obtained from four patients with osteogenic sarcoma receiving high-dose methotrexate/leucovorin rescue therapy consistently show the sustained elimination of 7-hydroxymethotrexate over several days, thus indicating the utility of specifically monitoring this nephrotoxic metabolite, at massive methotrexate doses.

Field desorption mass spectrometry in structural studies of polyene macrolide antibiotics: isolation and early identification of a pentaene macrolide antibiotic

Isolation of a pentaene macrolide antibiotic (NSC-277813) from Streptomyces griseus (FCRC-21) fermentation broth is described. Using field desorption mass spectrometry and high resolution field desorption mass spectrometry on the intact and derivatized antibiotic and degradation products, the antibiotic was identified as fungichromin. The application of field desorption mass spectrometry in the identification of polyene antibiotics is discussed.

Alamethicin biosynthesis: acetylation of the amino terminus and attachment of phenylalaninol

Alamethicin synthetase was extracted from the fungus Trichoderma viride at the end of its exponential growth phase. It is multienzyme complex with a molecular weight of approx. 480 000. The biosynthesis of alamethicin is initiated on the synthetase by acetylation of thiolester-bound aminoisobutyric acid, which remains enzyme bound. Acetyl-CoA serves as the acetate donor. Of the alamethicin constituents, glycine, alanine and valine are also acetylated when incubated alone. This acetylation is prevented by added aminoisobutyric acid, which indicates that the site on alamethicin synthetase catalyzing the acetylation has a preference for aminoisobutyric acid. Alamethicin formation on the synthetase is terminated by linkage of phenylalaninol to the carboxyl terminus of the peptide. It is unlikely that the amino alcohol is a degradation product of alamethicin or that it had been split off from the synthetase complex. Thus it is probably the reaction product of a separate enzyme system.