The liquidlike ordering of lipid A-diphosphate colloidal crystals: The influence of Ca2+, Mg2+, Na+, and K+ on the ordering of colloidal suspensions of lipid A-diphosphate in aqueous solutions

Trans-envelope multidrug efflux pumps of Gram-negative bacteria and their synergism with the outer membrane barrier

Antibiotic resistance is a serious threat to public health. Significant efforts are currently directed toward containment of the spread of resistance, finding new therapeutic options concerning resistant human and animal pathogens, and addressing the gaps in the fundamental understanding of mechanisms of resistance. Experimental data and kinetic modeling revealed a major factor in resistance, the synergy between active efflux and the low permeability barrier of the outer membrane, which dramatically reduces the intracellular accumulation of many antibiotics. The structural and mechanistic particularities of trans-envelope efflux pumps amplify the effectiveness of cell envelopes as permeability barriers. An important feature of this synergism is that efflux pumps and the outer membrane barriers are mechanistically independent and select antibiotics based on different physicochemical properties. The synergism amplifies even weak polyspecificity of multidrug efflux pumps and creates a major hurdle in the discovery and development of new therapeutics against Gram-negative pathogens.

Synergy between Active Efflux and Outer Membrane Diffusion Defines Rules of Antibiotic Permeation into Gram-Negative Bacteria

Gram-negative bacteria are notoriously resistant to antibiotics, but the extent of the resistance varies broadly between species. We report that in significant human pathogens Acinetobacter baumannii, Pseudomonas aeruginosa, and Burkholderia spp., the differences in antibiotic resistance are largely defined by their penetration into the cell. For all tested antibiotics, the intracellular penetration was determined by a synergistic relationship between active efflux and the permeability barrier. We found that the outer membrane (OM) and efflux pumps select compounds on the basis of distinct properties and together universally protect bacteria from structurally diverse antibiotics. On the basis of their interactions with the permeability barriers, antibiotics can be divided into four clusters that occupy defined physicochemical spaces. Our results suggest that rules of intracellular penetration are intrinsic to these clusters. The identified specificities in the permeability barriers should help in the designing of successful therapeutic strategies against antibiotic-resistant pathogens.IMPORTANCE Multidrug-resistant strains of Gram-negative pathogens rapidly spread in clinics. Significant efforts worldwide are currently directed to finding the rules of permeation of antibiotics across two membrane envelopes of these bacteria. This study created the tools for analysis of and identified the major differences in antibacterial activities that distinguish the permeability barriers of P. aeruginosa, A. baumannii, Burkholderia thailandensis, and B. cepacia We conclude that synergy between active efflux and the outer membrane barrier universally protects Gram-negative bacteria from antibiotics. We also found that the diversity of antibiotics affected by active efflux and outer membrane barriers is broader than previously thought and that antibiotics cluster according to specific biological determinants such as the requirement of specific porins in the OM, targeting of the OM, or specific recognition by efflux pumps. No universal rules of antibiotic permeation into Gram-negative bacteria apparently exist. Our results suggest that antibiotic clusters are defined by specific rules of permeation and that further studies could lead to their discovery.

Structural characterization in mixed lipid membrane systems by neutron and X-ray scattering

Lipids membranes, the primary component of the living cell, involve collective behaviour of numerous interacting molecules. The rich morphology and complex phase diagram of the lipid systems require different strategies in describing bio-membranes in order to capture the essential properties of self-assembly processes as well as the underling molecular collective phenomena involved in biological functions. Among the experimental methods used, the scattering techniques such as small angle neutrons and X-rays scattering (SANS and SAXS) are probably the most important experimental approaches for the structural investigation of bio-membranes and mixed lipids complex systems. In this tutorial review we describe the main approaches employed in the investigation of lipid bio-membranes by means of the neutron and x-ray scattering techniques. While introducing the main structural properties of lipid bio-membranes we highlight the important role of lipid components in different biological functions of living organisms. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Studies on structures of lipid A-monophosphate clusters

Single crystalline clusters of lipid A-monophosphate were grown from organic dispersions containing 5-15% (v/v) water at various volume fractions, φ, and temperatures. The morphology of the single lipid A-monophosphate crystals was either rhombohedral or hexagonal. The hexagonal crystals were needlelike or cylindrical in shape, with the long dimension parallel to the c axis of the unit cell. The crystalline clusters were studied using electron microscopy and x-ray powder diffraction. Employing molecular location methods following a Rietveld refinement and whole-pattern refinement revealed two monoclinic crystal structures in the space groups P2(1) and C2, both converged with R(F) = 0.179. The two monoclinic crystal structures were packing (hydrocarbon chains) and conformational (sugar) polymorphs. Neither of these two structures had been encountered previously. Only intramolecular hydrogen bonding was observed for the polymorphs, which were located between the amide and the carboxyl groups. Another crystalline structure was found in the volume-fraction range 2.00 × 10(-3) ≤ φ ≤ 2.50 × 10(-3), which displayed hexagonal symmetry. The hexagonal symmetry of the self-assembled lipid A-monophosphate crystalline phase might be reconciled with the monoclinic symmetry found at low-volume-fractions. Therefore, lowering the symmetry from cubic, i.e., Ia 3d, to rhombohedral R 3 m, and finally to the monoclinic space group C2 was acceptable if the lipid A-monophosphate anion was completely orientationally ordered.

Two new colloidal crystal phases of lipid A-monophosphate: order-to-order transition in colloidal crystals

A study of the structure of stable regular-shaped nanocrystals of hexa-acylated (C(14)) lipid A-monophosphate from Escherichia coli was carried out using dilute electrostatically stabilized aqueous dispersions at low ionic strength (I=1.0x10(-5)M NaCl). An order-to-order transition of colloidal clusters of lipid A-monophosphate was found at two volume fractions: phi=5.9x10(-4) and phi=11.5x10(-4). The clusters belonged to the cubic space groups Pm3n and Ia3d with unit-cell dimensions of a=4.55 nm and a=6.35 nm, respectively, as revealed by small-angle x-ray diffraction and electron-diffraction results of thin nanocrystals of lipid A-monophosphate. When viewed in the scanning electron microscope these fragile clusters displayed a number of shapes: cubic, cylindrical, and sometimes-rounded hexagons, which were extremely sensitive when exposed to an electron beam. The smallest and most numerous of the clusters appeared as approximately 7 nm cubes. Crystalline cluster formation occurred over a wide volume-fraction range, between 1.5x10(-4) and 40.0x10(-4), and at temperatures of 20 and 35 degrees C. The crystalline networks of the lipid A-monophosphate clusters may be represented by space-filling models of two pentagonal dodecahedra with six tetrakaidecahedra arrangements of lipid A-"micelles" in the cubic space group Pm3n. The simulated electron density profiles are in accord with spherical clusters of lipid A-monophosphate at the corners and at the body centers of the cubic Pm3n unit cell. The profiles are rounded tetrahedrally at distances of 1/4 and 3/4 along one of the bisectors of each face of the cubic unit cell. These nanocrystalline systems provide examples of "cellular" crystalline networks, which rearrange themselves spontaneously into three-dimensional polyhedral structures. It appears that a closely related analogy exists between the tetrahedrally close-packed networks as revealed for the lipid A-mono- and diphosphates [C. A. Faunce, H. Reichelt, H. H. Paradies, et al., J. Chem. Phys. 122, 214727 (2005); C. A. Faunce, H. Reichelt, P. Quitschau, et al., J. Chem. Phys. 127, 115103 (2007)]. However, the cubic Ia3d phase consists of two three-dimensional networks of rods, mutually intertwined but not connected. For this cubic Ia3d phase each junction involves three coplanar rods at an angle of 120 degrees, showing an interwoven labyrinth of lipid A-monophosphate rods which are connected three by three. The rod diameter is approximately 2.2 nm, which is similar in diameter to the disk-shaped aliphatic chiral core of lipid A-monophosphate (2.14 nm) with an ellipticity of 0.62 seen for the "c" position of the tetrakaidecahedra in the Pm3n cubic unit cell. An epitaxial relationship appears to exist between the {211} planes of the cubic Ia3d phase and the (001) planes of the lamellar phase as well as with the {10} planes of the hexagonal phase. The transformation of the cubic into the hexagonal phase can be reconciled by the growth of a cylinderlike assembly of lipid A-monophosphate molecules of the hexagonal phase parallel to the 111 directions of the cubic Ia3d phase. Upon cooling from 35 to 20 degrees C the cubic Ia3d lipid A-monophosphate phase unexpectedly transforms and gives rise to an intermediate R3m structure (a=3.90+/-0.12 nm, c=7.82+/-0.05 nm, and gamma=120 degrees). Both cubic Ia3d and hexagonal R3m phases originate from similar rodlike units of lipid A-monophosphate clusters. However, the overall shapes of the assemblies are different because of their spatial distribution. Both assemblies morphologically bridge the lipid A-monophosphate hexagonal and and lamellar phases. The structural path followed during the phase transitions is governed by topological similarities between the phase which forms and the one from which it originates. Although the two phases, Ia3d and R3m, have similar curvature energies on cooling, the topology is more than likely to be the initial factor determining the overall phase transition path.

Ordering of lipid A-monophosphate clusters in aqueous solutions

In this investigation, a study of the self-assembly of electrostatically stabilized aqueous dispersions of nanometric lipid A-monophosphate clusters from Escherichia coli was carried out in three different volume-fraction regimes. The experimental techniques used in the investigation were osmotic pressure, static and quasielastic light scattering, scanning electron microscopy and transmission electron microscopy, and small-angle x-ray scattering. Experiments were carried out at low ionic strength (I=0.1-5.0 mM NaCl) at 25 degrees C. At volume fractions between 1.5x10(-4)<or=phi<or=5.4x10(-4), the lipid A-monophosphate clusters had an average rms hydrodynamic diameter of d=7.5 nm, and a weighted-average molecular weight of (1.78+/-0.23)x10(5) g mol(-1). Quasielastic light scattering (LS) experiments yield similar values for the particle size and particle size distribution compared to electron microscopy, small-angle x-ray scattering, and LS experiments. When the volume fraction was increased to a higher regime 5.4x10(-4)<or=phi<or=9.50x10(-4), much larger clusters of lipid A monophosphate formed. The clusters detected in this volume-fraction range were assembled from between 8 and 52 of the d=7.5 nm clusters and the assemblies are densely packed in such a way that colloidal crystals composed of the monodisperse microspheres are in physical contact with their nearest neighbors. Clusters that formed in volume fractions between 10.0x10(-4)<or=phi<or=40.0x10(-4) revealed a weighted-average molecular weight of (10.15+/-0.17)x10(6) g mol(-1) and a hydrodynamic diameter of approximately d=70.6 nm. The crossover volume fraction between the small and the large clusters appeared at phicr=5.05x10(-4). In the intermediate volume-fraction range, the scattered intensity I(Q) vs Q curves (light and x rays) showed asymptotic behavior. From the asymptotic curves, the scattered intensity, the relationship between the average mass and radius, and the fractal dimension df were determined. The df value, which was evaluated from the expression I(Q) proportional, RGdf, was found to be 1.67+/-0.03, a value that was virtually independent of the ionic strength (0.1-5.0 mM NaCl) at 25 degrees C. Even at a very low ionic strength (I=0.10 mM NaCl), lipid A monophosphate formed a number of differently shaped clusters. Electron microscope images showed that two types of self-assembled clusters existed at the lowest volume-fraction range studied and also dominated the images taken at the higher volume-fraction regimes. One type of cluster showed a cubic morphology and a size variation of 50-100 nm, while another type took on the appearance of a quadratic cylinder, with dimensions of 50x150 nm2. The other clusters appeared in various shapes: dimers, trimers, and distorted tetramers, which were quite different from the ones previously observed for lipid A diphosphate. Small-angle x-ray diffraction experiments on lipid A-monophosphate clusters suspended in water, containing 5 mM NaCl (25 degrees C), indicated the existence of long-range order of d=7.5 nm. At low polydispersity, two distinct types of lipid A-monophosphate colloidal clusters were able to form at low polydispersity and were subsequently identified using light scattering, small-angle x-ray scattering, and selected-area electron diffraction. From an analysis of experimental results obtained from these clusters, distinct peaks could be assigned to a body-centered cubic (bcc) lattice, with a=49.5+/-1.8 nm. The solution structure found for lipid A diphosphate at volume fractions of 3.75x10(-4)<or=phi<or=4.15x10(-4) also exhibited a (bcc)-type lattice; however, a=36.1 nm [C. A. Faunceet al. J. Phys. Chem. 107, 2214 (2003)]. Using the particle and cluster properties determined from small-angle x-ray scattering, light scattering, and osmotic-pressure measurements as a function of volume fraction, good agreement was found between the directly measured osmotic-pressure values and those calculated from scattering experiments.

The rare crystallographic structure of d(CGCGCG)(2): the natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C

Several crystal structure analyses of complexes of synthetic polyamine compounds, including N(1)-(2-(2-aminoethylamino))ethyl)ethane-1,2-diamine PA(222) and N(1)-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA(2222), and left-handed Z-DNA d(CGCGCG)(2) have been reported. However, until now, there have been no examples of naturally occurring polyamines bound to the minor groove of the left-handed Z-DNA of d(CGCGCG)(2) molecule. We have found that spermidine, a natural polyamine, is connected to the minor groove of left-handed Z-DNA of d(CGCGCG)(2) molecule in a crystalline complex grown at 10 degrees C. The electron density of the DNA molecule was clear enough to determine that the spermidine was connected in the minor groove of two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2). This is the first example that a spermidine molecule can form a bridge conformation between two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2) in the minor groove.