Gramicidin, valinomycin, and cation permeability of Streptococcus faecalis

Cannabidiol increases gramicidin current in human embryonic kidney cells: An observational study

Gramicidin is a monomeric protein that is thought to non-selectively conduct cationic currents and water. Linear gramicidin is considered an antibiotic. This function is considered to be mediated by the formation of pores within the lipid membrane, thereby killing bacterial cells. The main non-psychoactive active constituent of the cannabis plant, cannabidiol (CBD), has recently gained interest, and is proposed to possess various potential therapeutic properties, including being an antibiotic. We previously determined that CBD’s activity on ion channels could be, in part, mediated by altering membrane biophysical properties, including elasticity. In this study, our goal was to determine the empirical effects of CBD on gramicidin currents in human embryonic kidney (HEK) cells, seeking to infer potential direct compound-protein interactions. Our results indicate that gramicidin, when applied to the extracellular HEK cell membrane, followed by CBD perfusion, increases the gramicidin current.

Properties of electrode-supported lipid cubic mesophase films with embedded gramicidin A: structure and ion-transport studies

The lipid cubic phase (LCP) is a nanomaterial composed of water channels surrounded by lipid bilayers. LCPs are stable at room temperature and are biocompatible. These features make the lipid cubic phases similar to biological membranes, and hence, are favorable for embedding membrane proteins. We show that the monoolein cubic phase deposited on the electrode forms a 3D lipid bilayer film convenient for electrochemical investigations of membrane proteins. In this research, we studied the effect of embedding an ionophoric peptide, gramicidin A (gA), on the structure and properties of the LCP film. The phase identity and structural parameters of the gramicidin-doped phase were characterized by small-angle X-ray scattering (SAXS). The potassium ion transport through the film were studied by electroanalytical methods: alternating current voltammetry (ACV), chronoamperometry (CA) and electrochemical impedance spectroscopy (EIS). Increased values for the current of the gramicidin-doped cubic phase compared to the empty cubic phase and changes of the EIS parameters confirmed that the peptide remained in the film in its active dimeric form. Our results show that the LCP can be considered a suitable 3D biomimetic film for the investigation of ion channels and other transporting membrane proteins, and for their application in electrochemical sensors.

The Nonribosomal Peptide Valinomycin: From Discovery to Bioactivity and Biosynthesis

Valinomycin is a nonribosomal peptide that was discovered from Streptomyces in 1955. Over the past more than six decades, it has received continuous attention due to its special chemical structure and broad biological activities. Although many research papers have been published on valinomycin, there has not yet been a comprehensive review that summarizes the diverse studies ranging from structural characterization, biogenesis, and bioactivity to the identification of biosynthetic gene clusters and heterologous biosynthesis. In this review, we aim to provide an overview of valinomycin to address this gap, covering from 1955 to 2020. First, we introduce the chemical structure of valinomycin together with its chemical properties. Then, we summarize the broad spectrum of bioactivities of valinomycin. Finally, we describe the valinomycin biosynthetic gene cluster and reconstituted biosynthesis of valinomycin. With that, we discuss possible opportunities for the future research and development of valinomycin.

Effect of charge status on the ion transport and antimicrobial activity of synthetic channels

The charge status of channels formed by pillararene–gramicidin hybrid molecules has a significant impact on their trans-membrane transport properties, membrane-association abilities and antimicrobial activities.

Host defense antimicrobial peptides as antibiotics: design and application strategies

This review deals with the design and application strategies of new antibiotics based on naturally occurring antimicrobial peptides (AMPs). The initial candidate can be designed based on three-dimensional structure or selected from a library of peptides from natural or laboratory sources followed by optimization via structure-activity relationship studies. There are also advanced application strategies such as induction of AMP expression from host cells by various factors (e.g., metals, amino acids, vitamin D and sunlight), the use of engineered probiotic bacteria to deliver peptides, the design of prodrug and peptide conjugates to improve specific targeting. In addition, combined uses of newly developed AMPs with existing antimicrobial agents may provide a practical avenue for effective management of antibiotic-resistant bacteria (superbugs), including biofilms. Finally, we highlight AMPs already in use or under clinical trials.

A unimolecular channel formed by dual helical peptide modified pillar[5]arene: correlating transmembrane transport properties with antimicrobial activity and haemolytic toxicity

Five unimolecular channels with different lengths are presented. The varying length of these channels has significant impact on their transport properties.

Multimerization of a Proline-Rich Antimicrobial Peptide, Chex-Arg20, Alters Its Mechanism of Interaction with the Escherichia coli Membrane

A3-APO, a de novo designed branched dimeric proline-rich antimicrobial peptide (PrAMP), is highly effective against a variety of in vivo bacterial infections. We undertook a selective examination of the mechanism for the Gram-negative Escherichia coli bacterial membrane interaction of the monomer (Chex-Arg20), dimer (A3-APO), and tetramer (A3-APO disulfide-linked dimer). All three synthetic peptides were effective at killing E. coli. However, the tetramer was 30-fold more membrane disruptive than the dimer while the monomer showed no membrane activity. Using flow cytometry and high-resolution fluorescent microscopy, it was observed that dimerization and tetramerization of the Chex-Arg20 monomer led to an alteration in the mechanism of action from non-lytic/membrane hyperpolarization to membrane disruption/depolarization. Our findings show that the membrane interaction and permeability of Chex-Arg20 was altered by multimerization.

Engineered biomaterial and biophysical stimulation as combinatorial strategies to address prosthetic infection by pathogenic bacteria

A plethora of antimicrobial strategies are being developed to address prosthetic infection. The currently available methods for implant infection treatment include the use of antibiotics and revision surgery. Among the bacterial strains, Staphylococcus species pose significant challenges particularly, with regard to hospital acquired infections. In order to combat such life threatening infectious diseases, researchers have developed implantable biomaterials incorporating nanoparticles, antimicrobial reinforcements, surface coatings, slippery/non-adhesive and contact killing surfaces. This review discusses a few of the biomaterial and biophysical antimicrobial strategies, which are in the developmental stage and actively being pursued by several research groups. The clinical efficacy of biophysical stimulation methods such as ultrasound, electric and magnetic field treatments against prosthetic infection depends critically on the stimulation protocol and parameters of the treatment modality. A common thread among the three biophysical stimulation methods is the mechanism of bactericidal action, which is centered on biophysical rupture of bacterial membranes, the generation of reactive oxygen species (ROS) and bacterial membrane depolarization evoked by the interference of essential ion-transport. Although the extent of antimicrobial effect, normally achieved through biophysical stimulation protocol is insufficient to warrant therapeutic application, a combination of antibiotic/ROS inducing agents and biophysical stimulation methods can elicit a clinically relevant reduction in viable bacterial numbers. In this review, we present a detailed account of both the biomaterial and biophysical approaches for achieving maximum bacterial inactivation. Summarizing, the biophysical stimulation methods in a combinatorial manner with material based strategies can be a more potent solution to control bacterial infections. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 2174-2190, 2017.

A combination of curcumin with either gramicidin or ouabain selectively kills cells that express the multidrug resistance-linked ABCG2 transporter

This paper introduces a strategy to kill selectively multidrug-resistant cells that express the ABCG2 transporter (also called breast cancer resistance protein, or BCRP). The approach is based on specific stimulation of ATP hydrolysis by ABCG2 transporters with subtoxic doses of curcumin combined with stimulation of ATP hydrolysis by Na(+),K(+)-ATPase with subtoxic doses of gramicidin A or ouabain. After 72 h of incubation with the drug combinations, the resulting overconsumption of ATP by both pathways inhibits the efflux activity of ABCG2 transporters, leads to depletion of intracellular ATP levels below the viability threshold, and kills resistant cells selectively over cells that lack ABCG2 transporters. This strategy, which was also tested on a clinically relevant human breast adenocarcinoma cell line (MCF-7/FLV1), exploits the overexpression of ABCG2 transporters and induces caspase-dependent apoptotic cell death selectively in resistant cells. This work thus introduces a novel strategy to exploit collateral sensitivity (CS) with a combination of two clinically used compounds that individually do not exert CS. Collectively, this work expands the current knowledge on ABCG2-mediated CS and provides a potential strategy for discovery of CS drugs against drug-resistant cancer cells.

Channel-forming bacterial toxins in biosensing and macromolecule delivery

To intoxicate cells, pore-forming bacterial toxins are evolved to allow for the transmembrane traffic of different substrates, ranging from small inorganic ions to cell-specific polypeptides. Recent developments in single-channel electrical recordings, X-ray crystallography, protein engineering, and computational methods have generated a large body of knowledge about the basic principles of channel-mediated molecular transport. These discoveries provide a robust framework for expansion of the described principles and methods toward use of biological nanopores in the growing field of nanobiotechnology. This article, written for a special volume on "Intracellular Traffic and Transport of Bacterial Protein Toxins", reviews the current state of applications of pore-forming bacterial toxins in small- and macromolecule-sensing, targeted cancer therapy, and drug delivery. We discuss the electrophysiological studies that explore molecular details of channel-facilitated protein and polymer transport across cellular membranes using both natural and foreign substrates. The review focuses on the structurally and functionally different bacterial toxins: gramicidin A of Bacillus brevis, α-hemolysin of Staphylococcus aureus, and binary toxin of Bacillus anthracis, which have found their "second life" in a variety of developing medical and technological applications.

Novel gramicidin formulations in cationic lipid as broad-spectrum microbicidal agents

Dioctadecyldimethylammonium bromide (DODAB) is an antimicrobial lipid that can be dispersed as large closed bilayers (LV) or bilayer disks (BF). Gramicidin (Gr) is an antimicrobial peptide assembling as channels in membranes and increasing their permeability towards cations. In mammalian cells, DODAB and Gr have the drawbacks of Gram-positive resistance and high toxicity, respectively. In this study, DODAB bilayers incorporating Gr showed good antimicrobial activity and low toxicity. Techniques employed were spectroscopy, photon correlation spectroscopy for sizing and evaluation of the surface potential at the shear plane, turbidimetric detection of dissipation of osmotic gradients in LV/Gr, determination of bacterial cell lysis, and counting of colony-forming units. There was quantitative incorporation of Gr and development of functional channels in LV. Gr increased the bilayer charge density in LV but did not affect the BF charge density, with localization of Gr at the BF borders. DODAB/Gr formulations substantially reduce Gr toxicity against eukaryotic cells and advantageously broaden the antimicrobial activity spectrum, effectively killing Escherichia coli and Staphylococcus aureus bacteria with occurrence of cell lysis.

Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin

Protein function is a complicated interplay between structure and dynamics, which can be heavily influenced by environmental factors and conditions. This is particularly true in the case of membrane proteins, such as the visual receptor rhodopsin. It has been well documented that lipid headgroups, polyunsaturated tails, and the concentration of cholesterol in membranes all play a role in the function of rhodopsin. Recently, we used all-atom simulations to demonstrate that different lipid species have preferential interactions and possible binding sites on rhodopsin's surface, consistent with experiment. However, the limited timescales of the simulations meant that the statistical uncertainty of these results was substantial. Accordingly, we present here 32 independent 1.6 μs coarse-grained simulations exploring lipids and cholesterols surrounding rhodopsin and opsin, in lipid bilayers mimicking those found naturally. Our results agree with those found experimentally and in previous simulations, but with far better statistical certainty. The results demonstrate the value of combining all-atom and coarse-grained models with experiment to provide a well-rounded view of lipid-protein interactions.

Cyclodepsipeptides as chemical tools for studying ionic transport through membranes

This paper reports a study of the chemistry of valinomycin, enniatins and related membrane-active depsipeptides that increase alkali metal ion permeability of model and biological membranes. The antimicrobial activity of these compounds and their effect on membranes has been correlated with their cation-complexing ability. The complexing reaction has been studied by spectropolarimetric and conductimetric methods. Nuclear magnetic resonance, optical rotatory dispersion, and infrared spectrophotometric studies have revealed the coexistence of conformers of the cyclodepsipeptides in solution and have led to elucidation of the spatial structure of valinomycin, enniatin B and their K(+) complexes. The effect of the conformational properties of the cyclodepsipeptides on their complexation efficiency and selectivity, surface-active properties and behavior towards phospholipid monolayers, bimolecular phospholipid membranes and a number of biological membrane systems has been ascertained. The studies have clearly shown the feasibility of using cyclodepsipeptides with predetermined structural and conformational parameters as chemical tools for membrane studies. it is suggested that the principle of conformation-dependent cation binding through iondipole interactions may possibly lie at the basis of the mode of action of systems governing the natural ion permeability in biological membranes.

Self-assembled, cation-selective ion channels from an oligo(ethylene glycol) derivative of benzothiazole aniline

This paper describes the spontaneous formation of well-defined pores in planar lipid bilayers from the self-assembly of a small synthetic molecule that contains a benzothiazole aniline (BTA) group attached to a tetra-ethylene glycol (EG4) moiety. Macroscopic and single-channel current recordings suggest that these pores are formed by the assembly of four BTA-EG4 monomers with an open pore diameter that appears similar to the one of gramicidin pores (~0.4 nm). The single-channel conductance of these pores is modulated by the pH of the electrolyte and has a minimum at pH~3. Self-assembled pores from BTA-EG4 are selective for monovalent cations and have long open channel lifetimes on the order of seconds. BTA-EG4 monomers in these pores appear to be arranged symmetrically across both leaflets of the bilayer, and spectroscopy studies suggest that the fluorescent BTA group is localized inside the lipid bilayers. In terms of biological activity, BTA-EG4 molecules inhibited growth of gram-positive Bacillus subtilis bacteria (IC50~50 μM) and human neuroblastoma SH-SY5Y cells (IC50~60 μM), while they were not toxic to gram-negative Escherichia coli bacteria at a concentration up to 500 μM. Based on these properties, this drug-like, synthetic, pore-forming molecule with a molecular weight below 500 g mol(-1) might be appealing as a starting material for development of antibiotics or membrane-permeating moieties for drug delivery. From a biophysical point of view, long-lived, well-defined ion-selective pores from BTA-EG4 molecules offer an example of a self-assembled synthetic supramolecule with biological function.

Comparative analysis of antimicrobial activities of valinomycin and cereulide, the Bacillus cereus emetic toxin

Cereulide and valinomycin are highly similar cyclic dodecadepsipeptides with potassium ionophoric properties. Cereulide, produced by members of the Bacillus cereus group, is known mostly as emetic toxin, and no ecological function has been assigned. A comparative analysis of the antimicrobial activity of valinomycin produced by Streptomyces spp. and cereulide was performed at a pH range of pH 5.5 to pH 9.5, under anaerobic and aerobic conditions. Both compounds display pH-dependent activity against selected Gram-positive bacteria, including Staphylococcus aureus, Listeria innocua, Listeria monocytogenes, Bacillus subtilis, and Bacillus cereus ATCC 10987. Notably, B. cereus strain ATCC 14579 and the emetic B. cereus strains F4810/72 and A529 showed reduced sensitivity to both compounds, with the latter two strains displaying full resistance to cereulide. Both compounds showed no activity against the selected Gram-negative bacteria. Antimicrobial activity against Gram-positive bacteria was highest at alkaline pH values, where the membrane potential (ΔΨ) is the main component of the proton motive force (PMF). Furthermore, inhibition of growth was observed in both aerobic and anaerobic conditions. Determination of the ΔΨ, using the membrane potential probe DiOC(2)(3) (in the presence of 50 mM KCl) in combination with flow cytometry, demonstrated for the first time the ability of cereulide to dissipate the ΔΨ in sensitive Gram-positive bacteria. The putative role of cereulide production in the ecology of emetic B. cereus is discussed.

Highly non-planar dendritic porphyrin for pH sensing: observation of porphyrin monocation

Metal-free porphyrin-dendrimers provide a convenient platform for the construction of membrane-impermeable ratiometric probes for pH measurements in compartmentalized biological systems. In all previously reported molecules, electrostatic stabilization (shielding) of the core porphyrin by peripheral negative charges (carboxylates) was required to shift the intrinsically low porphyrin protonation pK(a)'s into the physiological pH range (pH 6-8). However, binding of metal cations (e.g., K(+), Na(+), Ca(2+), Mg(2+)) by the carboxylate groups on the dendrimer could affect the protonation behavior of such probes in biological environments. Here we present a dendritic pH nanoprobe based on a highly non-planar tetraaryltetracyclohexenoporphyrin (Ar(4)TCHP), whose intrinsic protonation pK(a)'s are significantly higher than those of regular tetraarylporphyrins, thereby eliminating the need for electrostatic core shielding. The porphyrin was modified with eight Newkome-type dendrons and PEGylated at the periphery, rendering a neutral water-soluble probe (TCHpH), suitable for measurements in the physiological pH range. The protonation of TCHpH could be followed by absorption (e.g., ε(Soret)(dication)∼270,000 M(-1) cm(-1)) or by fluorescence. Unlike most tetraarylporphyrins, TCHpH is protonated in two distinct steps (pK(a)'s 7.8 and 6.0). In the region between the pK(a)'s, an intermediate species with a well-defined spectroscopic signature, presumably a TCHpH monocation, could be observed in the mixture. The performance of TCHpH was evaluated by pH gradient measurements in large unilamellar vesicles. The probe was retained inside the vesicles and did not pass through and/or interact with vesicle membranes, proving useful for quantification of proton transport across phospholipid bilayers. To interpret the protonation behavior of TCHpH we developed a model relating structural changes on the porphyrin macrocycle upon protonation to its basicity. The model was validated by density functional theory (DFT) calculations performed on a planar and non-planar porphyrin, making it possible to rationalize higher protonation pK(a)'s of non-planar porphyrins as well as the easier observation of their monocations.

Role of Na+and K+in Enzyme Function

Metal complexation is a key mediator or modifier of enzyme structure and function. In addition to divalent and polyvalent metals, group IA metals Na+and K+play important and specific roles that assist function of biological macromolecules. We examine the diversity of monovalent cation (M+)-activated enzymes by first comparing coordination in small molecules followed by a discussion of theoretical and practical aspects. Select examples of enzymes that utilize M+as a cofactor (type I) or allosteric effector (type II) illustrate the structural basis of activation by Na+and K+, along with unexpected connections with ion transporters. Kinetic expressions are derived for the analysis of type I and type II activation. In conclusion, we address evolutionary implications of Na+binding in the trypsin-like proteases of vertebrate blood coagulation. From this analysis, M+complexation has the potential to be an efficient regulator of enzyme catalysis and stability and offers novel strategies for protein engineering to improve enzyme function.

Amino Acid Derived Macrocycles—An Area Driven by Synthesis or Application?

The synthesis, structure, and physical properties of macrocycles have fascinated chemists for many years. Their inherent properties make them useful in areas as diverse as ion transport across membranes, development of new antibiotics, and catalysis. In this Review, the authors examine the chemistry of macrocycles containing non-peptidic amino acid derived molecules; the analysis is discussed in terms of function, rather than structure or synthesis. It is revealed that the diverse and imaginative structures created by synthetic chemists are not being fully exploited in application-driven endeavors.

Gramicidin channels

Gramicidin channels are mini-proteins composed of two tryptophan-rich subunits. The conducting channels are formed by the transbilayer dimerization of nonconducting subunits, which are tied to the bilayer/solution interface through hydrogen bonds between the indole NH groups and the phospholipid backbone and water. The channel structure is known at atomic resolution and the channel's permeability characteristics are particularly well defined: gramicidin channels are selective for monovalent cations, with no measurable permeability to anions or polyvalent cations; ions and water move through a pore whose wall is formed by the peptide backbone; and the single-channel conductance and cation selectivity vary when the amino acid sequence is varied, even though the permeating ions make no contact with the amino acid side chains. Given the amount of experimental information that is available--for both the wild-type channels and for channels formed by amino acid-substituted gramicidin analogues--gramicidin channels provide important insights into the microphysics of ion permeation through bilayer-spanning channels. For the same reason, gramicidin channels constitute the system of choice for evaluating computational strategies for obtaining mechanistic insights into ion permeation through the complex channels formed by integral membrane proteins.

Correlation of bilayer membrane cation transport and biological activity in alkyl-substituted lariat ethers

Dialkyldiaza-18-crown-6 lariat ethers having twin n-octyl, n-decyl, n-dodecyl, n-tetradecyl, n-hexadecyl, 1-oxodecyl and 1-oxododecyl side arms were prepared and studied. Cation transport in liposomes mediated by these compounds showed discontinuous activity that correlated with toxicity to the bacteria E. coli and B. Subtilis, and the yeast S. Cerevisiae. Transport, toxicity and membrane depolarization studies all suggest that side chain length affords very different interactions in a bilayer membrane compared with bulk phases. An explanation for activity in terms of carrier transport and restricted transverse relaxation is proposed.

Porphyrin and tetrabenzoporphyrin dendrimers: tunable membrane-impermeable fluorescent pH nanosensors

The pH dependencies of the UV-vis and fluorescent spectra of new water-soluble dendritic porphyrins and tetrabenzoporphyrins were studied. Because of extended pi-conjugation and nonplanar distortion, the absorption and the emission bands of tetraaryltetrabenzoporphyrins (Ar(4)TBP) are red-shifted and do not overlap with those of regular tetraarylporphyrins (Ar(4)P). When encapsulated inside dendrimers with hydrophilic outer layers, Ar(4)Ps and Ar(4)TBPs become water soluble and can serve as pH indicators, with pK's adjustable by the peripheral charges on the dendrimers. Two new dendritic porphyrins, Gen 4 polyglutamic porphyrin dendrimer H(2)P-Glu(4)OH (1) with 64 peripheral carboxylates and Gen 1 poly(ester amide) Newkome-type tetrabenzoporphyrin dendrimer H(2)TBP-Nw(1)OH (2) with 36 peripheral carboxylates, were synthesized and characterized. The pK's of the encapsulated porphyrins (pK(H)()2(P)(-)(Glu)()4(OH) = 6.2 and pK(H)()2(TBP)(-)(Nw)()1(OH) = 6.3) were found to be strongly influenced by the dendrimers, revealing significant electrostatic shielding of the cores by the peripheral charges. The titration curves obtained by differential excitation using the mixtures of the dendrimers were shown to be identical to those determined for the dendrimers individually. Due to their peripheral carboxylates and nanometric molecular size, porphyrin dendrimers cannot penetrate through phospholipid membranes. Dendrimer 1 was captured inside phospholipid liposomes, which were suspended in a solution containing dendrimer 2. No response from 1 was detected upon pH changes in the bulk solution, while the response from 2 was predictably strong. When proton channels were created in the liposome walls, both compounds responded equally to the bulk pH changes. These results suggest that porphyrin dendrimers can be used as fluorescent pH indicators for proton gradient measurements.

Solid-state 19F-NMR analysis of 19F-labeled tryptophan in gramicidin A in oriented membranes

The response of membrane-associated peptides toward the lipid environment or other binding partners can be monitored by solid-state NMR of suitably labeled side chains. Tryptophan is a prominent amino acid in transmembrane helices, and its (19)F-labeled analogues are generally biocompatible and cause little structural perturbation. Hence, we use 5F-Trp as a highly sensitive NMR probe to monitor the conformation and dynamics of the indole ring. To establish this (19)F-NMR strategy, gramicidin A was labeled with 5F-Trp in position 13 or 15, whose chi(1)/chi(2) torsion angles are known from previous (2)H-NMR studies. First, the alignment of the (19)F chemical shift anisotropy tensor within the membrane was deduced by lineshape analysis of oriented samples. Next, the three principal axes of the (19)F chemical shift anisotropy tensor were assigned within the molecular frame of the indole ring. Finally, determination of chi(1)/chi(2) for 5F-Trp in the lipid gel phase showed that the side chain alignment differs by up to 20 degrees from its known conformation in the liquid crystalline state. The sensitivity gain of (19)F-NMR and the reduction in the amount of material was at least 10-fold compared with previous (2)H-NMR studies on the same system and 100-fold compared with (15)N-NMR.

Measuring the dielectric properties of herpes simplex virus type 1 virions with dielectrophoresis

An investigation has been performed into the biophysical properties of the enveloped mammalian virus, herpes simplex virus type 1 (HSV-1). The dielectrophoretic behaviour of the virus particles was measured as a function of applied frequency (over the range 100 kHz-20 MHz) and conductivity of the suspending medium (over the range 1-100 mS m(-1)). The dielectric properties of the virus were determined from the dielectrophoretic data using the smeared-out shell model. The data suggest that the intact particle has a surface conductance of 0.3 nS, an internal and membrane permittivity of 75varepsilon(o) and 7.5varepsilon(o), respectively, an internal conductivity of approximately 0.1 S m(-1) and a zeta potential of 70 mV. The dielectric properties were measured for intact, fresh virus particles and also for particles following exposure to various modifying agents, such as treatment with enzymes, ionophores and ageing. It is shown that the observed changes in the dielectrophoretic spectrum, and the variations in the dielectric properties of the virus concur with the expected physiological effects of these agents.

High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints

BACKGROUND

Solid-state nuclear magnetic resonance (NMR) spectroscopy provides novel structural constraints from uniformly aligned samples. These orientational constraints orient specific atomic sites with respect to the magnetic field direction and the unique molecular axis of alignment. Solid-state NMR is uniquely and ideally suited for providing such structural constraints on polypeptides and proteins in a lamellar phase lipid environment. Membrane protein structure represents a great challenge for structural biologists; a new approach for characterizing high resolution three-dimensional structure in such an environment is needed.

RESULTS

The optimal use of orientational constraints for defining three-dimensional structures is demonstrated with the elucidation of the gramicidin A channel structure at high resolution. Initial structures are refined against both the experimental constraints and the CHARMM energy using a novel simulated-annealing protocol to define torsion angle solutions with an error bar of approximately +/- 5 degrees.

CONCLUSIONS

This analysis results in the determination of a high-resolution, time averaged structure of gramicidin A obtained in a lipid bilayer environment above the gel-to-liquid crystalline phase transition temperature. It is demonstrated that solid-state NMR can be used to establish polypeptide, and potentially protein, structures in such an environment. Furthermore, this high-resolution structure is demonstrated to provide new insights into polypeptide function. For the gramicidin A channel the roles of the indole groups that facilitate ion transport and details of the cation solvation environment provided by the amide oxygens are characterized.

Binding of alkaline cations to the double-helical form of gramicidin

Gramicidin is a polypeptide antibiotic that forms monovalent cation-specific channels in membrane environments. In organic solvents and in lipids containing unsaturated fatty acid chains, it forms a double-helical "pore" structure, in which two monomers are intertwined. This form of gramicidin can bind two cations inside its lumen, and the crystal structures of both an ion complex and an ion-free form have been determined. In this study, we have used circular dichroism (CD) spectroscopy to examine the binding mechanism and the binding constants (K1 and K2) of cations to gramicidin in the double helical form in methanol solution. The dramatic change in optical rotation in the far-ultraviolet CD spectrum of gramicidin provides a useful tool for monitoring the binding. The binding mechanism appears to involve a large conformation change associated with the binding of ions to the first of the two sites. The calculated values for the K1 binding constants for alkaline cations are considerably smaller than the K2 binding constants. The order of binding affinity for alkaline cations is similar to that for the helical dimer "channel" form of gramicidin, i.e., Cs+ approximately Rb+ > > K+ > Li+, but in comparison to the helical dimer form, the binding to double-helical dimers is dominated by a cation size-dependent conformational change in the gramicidin structure.

Nisin as a model food preservative

Nisin is a ribosomally synthesized peptide that has broad-spectrum antibacterial activity, including activity against many bacteria that are food-spoilage pathogens. Nisin is produced as a fermentation product of a food-grade bacterium, and the safety and efficacy of nisin as a food preservative have resulted in its widespread use throughout the world, including the U.S. Nisin is a member of the class of antimicrobial substances known as lantibiotics, so called because they contain the unusual amino acid lanthionine. Lantibiotics, in general, have considerable promise as food preservatives, although only nisin has been sufficiently well characterized to be used for this purpose. As the number of known natural lantibiotics has increased and their useful characteristics have been explored, it has become desirable to synthesize structural analogs of nisin and other lantibiotics that do not occur naturally. The fact that lantibiotics are gene-encoded peptides synthesized by transcription and translation allows structural variants to be generated by mutagenesis. This review focuses on the progress that has been made in the construction and biological expression of genetically engineered nisin structural analogs. For example, a host-vector pair has been engineered that permits the construction of mutants of the structural gene for subtilin, which is a naturally occurring structural analog of nisin. The vector is designed in such a way that the mutant gene can be substituted for the natural subtilin gene in the chromosome of Bacillus subtilis, which in turn directs the transcription, translation, posttranslational modifications, and secretion of the mature form of the structural analog. Several structural analogs have been constructed, and their properties have provided insight into some of the structure-function relationships in lantibiotics, as well as their mechanism of antimicrobial action. These advances are assessed together with potential problems in the future development of nisin analogs as valuable new food preservatives.

The pore dimensions of gramicidin A

The ion channel forming peptide gramicidin A adopts a number of distinct conformations in different environments. We have developed a new method to analyze and display the pore dimensions of ion channels. The procedure is applied to two x-ray crystal structures of gramicidin that adopt distinct antiparallel double helical dimer conformations and a nuclear magnetic resonance (NMR) structure for the beta6.3 NH2-terminal to NH2-terminal dimer. The results are discussed with reference to ion conductance properties and dependence of pore dimensions on the environment.

The antimicrobial effect of a structural variant of subtilin against outgrowing Bacillus cereus T spores and vegetative cells occurs by different mechanisms

Subtilin is a ribosomally synthesized antimicrobial peptide that contains several unusual amino acids as a result of posttranslational modifications. Site-directed mutagenesis was employed to construct a structural variant of subtilin in which the unusual dehydroalanine (Dha) residue at position 5 was changed to alanine. Proton nuclear magnetic resonance spectroscopy, amino acid composition, and N-terminal sequence analysis established that the mutation did not disrupt posttranslational processing of the precursor peptide. This mutant subtilin was devoid of antimicrobial activity as assessed by its lack of inhibitory effects on outgrowth of Bacillus cereus T spores. However, this same mutant subtilin was fully active with respect to its ability to induce lysis of vegetative B. cereus T cells. Because an intact Dha-5 residue is required in the one instance but not in the other, it was concluded that the molecular mechanism by which subtilin inhibits (without lysis) spore outgrowth is not the same as the mechanism by which it inhibits (with lysis) vegetative cells.

Quantitative determination of the intracellular concentration of the various forms of HPr, a phosphocarrier protein of the phosphoenolpyruvate: sugar phosphotransferase system in growing cells of oral streptococci

A simple procedure for quantitative estimation of the different phosphorylated forms of the phosphocarrier protein HPr in growing cells of oral streptococci is described. The growth of the cells was rapidly stopped by acidification of the medium and concomitant addition of the ionophore Gramicidin D. This procedure inactivated Enzyme I, HPr(Ser) kinase, HPr(Ser-P) phosphatase, and the enzymes involved in the metabolism of the allosteric effectors as well as the substrates of HPr phosphorylation. The cellular concentrations of HPr (His approximately P), HPr (Ser-P), HPr (His approximately P) (Ser-P), and free HPr were then determined by crossed immunoelectrophoresis.

Monoclinic uncomplexed double-stranded, antiparallel, left-handed beta 5.6-helix (increases decreases beta 5.6) structure of gramicidin A: alternate patterns of helical association and deformation

A comparison of the monoclinic and orthorhombic crystal structures of the uncomplexed double-stranded, antiparallel, left-handed beta-helix (5.6 amino acid residues per turn) (increases decreases beta 5.6) conformers of gramicidin A reveals marked differences in the tryptophan side-chain orientations and the degree of helical uniformity of the dimer and in the manner in which these helical dimers associate with one another in the crystal. The helix of the orthorhombic dimer exhibits a regular pattern of bulges and constrictions that appears to be induced by crystal packing forces affecting tryptophan side chains that are aligned parallel to the helix axis. The monoclinic dimer is more uniform than the orthorhombic dimer as a consequence of pi stacking interactions between dimers in which orientation of tryptophan side chains is normal to the helix axis to relieve the lateral crystal packing forces that may locally twist and deform the helix. It may be inferred from these observations that lipid interactions may be expected to destabilize the increases decreases beta 5.6 helix when it is inserted into a membrane bilayer.

Growth inhibition of Plasmodium falciparum in in vitro cultures by selective action of tryptophan-N-formylated gramicidin incorporated in lipid vesicles

We studied the differential effect of tryptophan-N-formylated gramicidin on uninfected and Plasmodium falciparum-infected erythrocytes. Trp-N-formylated gramicidin induces a much faster leakage of K+ from infected cells than from uninfected cell whereas, and at an even lower concentration, gramicidin A' causes a rapid K+ leakage from both uninfected and infected cells. We also studied the effect of Trp-N-formylated gramicidin and gramicidin A' incorporated in liposomes on the growth of Plasmodium falciparum in an in vitro culture. Incorporation of Trp-N-formylated gramicidin in the membranes of so-called 'stealth' vesicles strongly decreases the concentration needed to induce 50% inhibition of parasite growth. Moreover, no decrease in the K+ content of uninfected cells was observed when cells were exposed to liposome-incorporated Trp-N-formylated gramicidin at a concentration which causes full inhibition of parasite growth. These observations strongly suggest that Trp-N-formylated gramicidin incorporated in 'stealth' vesicles ends up specifically in the infected cell, thereby inhibiting the growth of the growth of the malaria parasite.

Mechanism and regulation of phosphate transport in Streptococcus pyogenes

In contrast to results reported with other bacteria, uptake of 32Pi in Streptococcus pyogenes was found to occur rapidly in starved cultures and to be strongly and immediately inhibited by addition of exogenous glycolytic energy sources (such as glucose) and nonglycolytic sources of ATP (such as arginine). Preincubation of starved cells with NaF, iodoacetate, or arsenate eliminated the inhibiting effect of glucose but not that of arginine. In accordance with the hypothesis that transport was attributable to Pi-Pi exchange, uptake and efflux of 32Pi in the presence of trans unlabeled Pi exhibited similar characteristics and were largely eliminated by reduction of the trans Pi concentration. Neither process was inhibited appreciably by pretreatment of cells with ionophores or metabolic inhibitors, but both processes were abolished by exposure to p-chloromercuribenzoate. Inhibition by both exogenous energy sources resulted in a reduction in the maximal velocity of transport (Vmax). Whereas arginine also caused a shift in the apparent Michaelis-Menten constant (Km) to larger values, glucose did not alter the Km. On the basis of the results reported, we propose that the rate of Pi exchange is determined positively by the intracellular and extracellular concentrations of Pi and negatively by ATP or metabolites thereof. The mechanism of ATP action is unknown but could involve either covalent or noncovalent modification of the carrier protein.

Temperature-jump and voltage-jump experiments at planar lipid membranes support an aggregational (micellar) model of the gramicidin A ion channel

The kinetics of formation and dissociation of channels formed by gramicidin A and two analogues in planar lipid membranes was studied using a laser temperature-jump technique developed earlier [Brock, W., Stark, G., Jordan, P.C. (1981), Biophys. Chem. 13:329-348]. The time course of the electric current was found to agree with a single exponential term plus a linear drift. In case of gramicidin A the relaxation time was identical to that reported for V-jump experiments [Bamberg, E., Läuger, P. (1973), J. Membrane Biol. 11:177-194], which were interpreted on the basis of a dimerization reaction. The same results were obtained for gramicidin A and for chemically dimerized malonyl-bis-desformylgramicidin. It is therefore suggested that the dimerization represents a parallel association of two dimers to a tetramer. There is evidence that the tetramer, contrary to the presently favored dimer hypothesis, is the smallest conductance unit of an active gramicidin channel. An additional V-jump-induced relaxation process of considerably larger time constant is interpreted as a further aggregation of gramicidin dimers.

Effect of gramicidin D on the acidogenic properties of oral streptococci and human dental plaque

The effect of gramicidin D, Gramicidin S, and carbonylcyanide p-trifluoromethoxyphenyl hydrazone on the glycolysis of various oral streptococci was investigated. Gramicidin D was the most effective and inhibited the glycolysis of all the streptococci studied in the presence of the most common sugars found in man's diet (sucrose, lactose, glucose, and fructose). A concentration of 2.5 X 10(-6) M gramicidin D was sufficient to decrease significantly the rate of glycolysis of human dental plaque in the presence of sucrose. The use of this ionophore as a caries preventive agent is discussed.

An interaction between gramicidin and the sigma subunit of RNA polymerase

Gramicidin, a peptide antibiotic produced by Bacillus brevis, inhibits initiation of transcription by RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6). We show here that the presence of gramicidin causes an increase in the rate of cleavage of the sigma subunit of Escherichia coli RNA polymerase by trypsin, although it does not alter the cleavage rate of any of the core subunits. Furthermore, whereas isolated sigma is cleaved much faster than is sigma in holoenzyme, gramicidin substantially decreases the trypsin cleavage rate of isolated sigma. Inhibition of RNA polymerase activity by gramicidin in consistent with a sigma-specific effect: the antibiotic is a strong inhibitor of transcription of T7 phage DNA, which requires sigma for activity, but it has little effect on transcription of sigma-independent templates, such as poly(dA-dT).poly)dA-dT) and calf thymus DNA. These results are discussed in light of the hypothesized role for gramicidin in the initiation of sporulation of B. brevis.