Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus.

Ribosome biogenesis is an energy-intense multistep process where even minimal defects can cause severe phenotypes up to cell death. Ribosome assembly is facilitated by biogenesis factors such as ribosome assembly factors. These proteins facilitate the interaction of ribosomal proteins with rRNA and correct rRNA folding. One of these maturation factors is RimP which is required for efficient 16S rRNA processing and 30S ribosomal subunit assembly. Here, we describe the binding mode of Staphylococcus aureus RimP to the small ribosomal subunit and present a 4.2 Å resolution cryo-EM reconstruction of the 30S-RimP complex. Together with the solution structure of RimP solved by NMR spectroscopy and RimP-uS12 complex analysis by EPR, DEER, and SAXS approaches, we show the specificity of RimP binding to the 30S subunit from S. aureus. We believe the results presented in this work will contribute to the understanding of the RimP role in the ribosome assembly mechanism.

Electrochemical Properties and Structure of Membranes from Perfluorinated Copolymers Modified with Nanodiamonds.

In this study, we aimed to design and research proton-conducting membranes based on Aquivion®-type material that had been modified with detonation nanodiamonds (particle size 4-5 nm, 0.25-5.0 wt. %). These nanodiamonds carried different functional groups (H, OH, COOH, F) that provided the hydrophilicity of the diamond surface with positive or negative potential, or that strengthened the hydrophobicity of the diamonds. These variations in diamond properties allowed us to find ways to improve the composite structure so as to achieve better ion conductivity. For this purpose, we prepared three series of membrane films by first casting solutions of perfluorinated Aquivion®-type copolymers with short side chains mixed with diamonds dispersed on solid substrates. Then, we removed the solvent and the membranes were structurally stabilized during thermal treatment and transformed into their final form with -SO3H ionic groups. We found that the diamonds with a hydrogen-saturated surface, with a positive charge in aqueous media, contributed to the increase in proton conductivity of membranes to a greater rate. Meanwhile, a more developed conducting diamond-copolymer interface was formed due to electrostatic attraction to the sulfonic acid groups of the copolymer than in the case of diamonds grafted with negatively charged carboxyls, similar to sulfonic groups of the copolymer. The modification of membranes with fluorinated diamonds led to a 5-fold decrease in the conductivity of the composite, even when only a fraction of diamonds of 1 wt. % were used, which was explained by the disruption in the connectivity of ion channels during the interaction of such diamonds mainly with fluorocarbon chains of the copolymer. We discussed the specifics of the mechanism of conductivity in composites with various diamonds in connection with structural data obtained in neutron scattering experiments on dry membranes, as well as ideas about the formation of cylindrical micelles with central ion channels and shells composed of hydrophobic copolymer chains. Finally, the characteristics of the network of ion channels in the composites were found depending on the type and amount of introduced diamonds, and correlations between the structure and conductivity of the membranes were established.

Anionic lipids modulate little the reorganization effect of amyloid-beta peptides on membranes.

Amyloid-ß peptide interactions with model lipid membranes have been studied by means of small angle neutron scattering and molecular dynamics simulations. These interactions had been indicated recently as an origin of the membrane structure reorganizations between spherical small unilamellar vesicles and planar bicelle-like structures. In present work, we investigate the influence of charge on the peptide-triggered morphological changes by introducing the anionic lipid DMPS to the underlying DMPC membrane. Changes to the membrane thickness and the overall membrane structure with and without Aß25-35 incorporated have been investigated over a wide range of temperatures. Our results document the previously reported morphological reformations between bicelle-like structures present in gel phase and small unilamellar vesicles present in fluid phase to be independent from the charge existence in the system.

Hybrid Polymer-Surfactant Wormlike Micelles for Concurrent Use for Oil Recovery and Drag Reduction.

We report on the effect of a hydrocarbon (n-dodecane) on the rheological properties and shapes of the hybrid wormlike micelles (WLMs) of a surfactant potassium oleate with an embedded polymer poly(4-vinylpyridine). With and without hydrocarbon solutions, the hybrid micelles exhibit the same values of viscosity at shear rates typical for hydraulic fracturing (HF) tests, as solutions of polymer-free WLMs. Therefore, similar to WLMs of surfactants, they could be applied as thickeners in HF fluids without breakers. At the same time, in the presence of n-dodecane, the hybrid micelles have much higher drag-reducing efficiency compared to microemulsions formed in polymer-free systems since they form "beads-on-string" structures according to results obtained using cryo-transmission electron microscopy (cryo-TEM), dynamic-light scattering (DLS), and small-angle X-ray scattering (SAXS). Consequently, they could also act as drag-reducing agents in the pipeline transport of recovered oil. Such a unique multi-functional additive to a fracturing fluid, which permits its concurrent use in oil production and oil transportation, has not been proposed before.

Caught red handed: modeling and confirmation of the myeloperoxidase ceruloplasmin alpha-thrombin complex.

The work is devoted to the study of the structural characteristics of the myeloperoxidase-ceruloplasmin-thrombin complex using small-angle neutron scattering methods in combination with computer modeling, as well as surface plasmon resonance and solid-phase enzyme assay. We have previously shown that the functioning of active myeloperoxidase during inflammation, despite the presence in the blood of an excess of ceruloplasmin which inhibits its activity, is possible due to the partial proteolysis of ceruloplasmin by thrombin. In this study, the myeloperoxidase-ceruloplasmin-thrombin heterohexamer was obtained in vitro. The building of a heterohexamer full-atomic model in silico, considering the glycosylation of the constituent proteins, confirmed the absence of steric barriers for the formation of protein-protein contacts. It was shown that the partial proteolysis of ceruloplasmin does not affect its ability to bind to myeloperoxidase, and a structural model of the heterohexamer was obtained using the small-angle neutron scattering method.

Study of Physico-Chemical Properties and Morphology of Phospholipid Composition of Indomethacin.

Nonsteroidal anti-inflammatory drugs (NSAIDs), inhibitors of cyclooxygenase-2, an enzyme involved in the formation of anti-inflammatory prostaglandin PGE2, are the most common treatment for chronic inflammatory diseases, such as, for example, arthritis. One of the most commonly used drugs of this class is indomethacin, a derivative of indolylacetic acid. In this work, we studied the physicochemical properties of the phospholipid composition of indomethacin obtained earlier (codenamed "Indolip") and the effect of freeze drying on its parameters. It was shown that the properties such as particle size, light transmission, phospholipid oxidation index did not change significantly, which indicated the stability of the drug after lyophilization. Measurement of the spectra of small-angle neutron scattering has shown that morphologically, Indolip is a vesicle whose radius is five times greater than the value of the bilayer thickness.

Cations Do Not Alter the Membrane Structure of POPC-A Lipid With an Intermediate Area.

Combining small-angle neutron scattering (SANS), small-angle X-ray scattering (SAXS), and densitometric measurements, we have studied the interactions of the divalent cations Ca2+ and Mg2+ with the lipid vesicles prepared of a mixed-chain palmitoyl-oleoyl-phosphatidylcholine (POPC) at 25°C. The structural parameters of the POPC bilayer, such as the bilayer thickness, lateral area, and volume per lipid, displayed no changes upon the ion addition at concentrations up to 30 mM and minor changes at > 30 mM Ca2+ and Mg2+, while some decrease in the vesicle radius was observed over the entire concentration range studied. This examination allows us to validate the concept of lipid-ion interactions governed by the area per lipid suggested previously and to propose the mixed mode of those interactions that emerge in the POPC vesicles. We speculate that the average area per POPC lipid that corresponds to the cutoff length of lipid-ion interactions generates an equal but opposite impact on ion bridges and separate lipid-ion pairs. As a result of the dynamic equilibrium, the overall structural properties of bilayers are not affected. As the molecular mechanism proposed is affected by the structural properties of a particular lipid, it might help us to understand the fundamentals of processes occurring in complex multicomponent membrane systems.

Ordered Mesoporous Silica Prepared in Different Solvent Conditions: Application for Cu(II) and Pb(II) Adsorption.

In this work, the synthesis of ordered mesoporous silica of MCM-41 type was investigated aimed at improving its morphology by varying the synthesis conditions in a one-pot process, employing different temperatures and solvent conditions. 2-methoxyethanol was used as co-solvent to ethanol. The co-solvent ratio and the synthesis temperature were varied. The pore morphology of the materials was characterized by nitrogen porosimetry and small angle neutron scattering (SANS), and the particle morphology by transmission electron microscopy (TEM) and ultra-small angle neutron scattering (USANS). The thermal behavior was investigated by simultaneous thermogravimetry-differential scanning calorimetry (TG-DSC) measurements. The SANS and N2 sorption results demonstrated that a well-ordered mesoporous structure was obtained at all conditions in the synthesis at room temperature. Addition of methoxyethanol led to an increase of the pore wall thickness. Simultaneously, an increase of methoxyethanol content led to lowering of the mean particle size from 300 to 230 nm, according to the ultra-small angle scattering data. The ordered porosity and high specific surfaces make these materials suitable for applications such as adsorbents in environmental remediation. Batch adsorption measurements of metal ion removal from aqueous solutions of Cu(II) and Pb(II) showed that the materials exhibit dominantly monolayer surface adsorption characteristics. The adsorption capacities were 9.7 mg/g for Cu(II) and 18.8 mg/g for Pb(II) at pH 5, making these materials competitive in performance to various composite materials.

Mechanisms of membrane protein crystallization in 'bicelles'.

Despite remarkable progress, mainly due to the development of LCP and 'bicelle' crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the "bicelle" crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of "bicelle" MP crystallization and will support rational design of crystallization.

Structure and Intermolecular Interactions in Aqueous Solutions of Polyethylene Glycol.

Aqueous solutions of polyethylene glycol are studied by small-angle neutron scattering over a broad range of polymer molecular masses and concentrations. The scattering data were modeled by a Gaussian chain form factor combined with random phase approximation, which provided good fits over the whole studied concentration range. The results showed that polyethylene glycol in the molecular mass range 0.4-20 kDa in water at physiological temperature T = 37 °C behaves like a random coil in nearly theta solvent conditions. The obtained results serve as a reference for the description of complex mixtures with PEG used in various applications.

Amyloid-beta peptide (25-35) triggers a reorganization of lipid membranes driven by temperature changes.

The amyloid-beta peptide (Aß) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of temperature on the latter interactions by evaluating the structural characteristics of zwitterionic phosphatidylcholine (PC) membranes with incorporated Aß25-35 peptide. By means of small angle neutron scattering (SANS), we have observed for the first time a spontaneous reformation of extruded unilamellar vesicles (EULVs) to discoidal bicelle-like structures (BLSs) and small unilamellar vesicles (SULVs). These changes in the membrane self-organization happen during the thermodynamic phase transitions of lipids and only in the presence of the peptide. We interpret the dramatic changes in the membrane's overall shape with parallel changes in its thickness as the Aß25-35 triggered membrane damage and a consequent reorganization of its structure. The suggested process is consistent with an action of separate peptides or small size peptide oligomers rather than the result of large Aß fibrils.

Composite Films of HDPE with SiO2 and ZrO2 Nanoparticles: The Structure and Interfacial Effects.

Herein, we investigated the influence of two types of nanoparticle fillers, i.e., amorphous SiO2 and crystalline ZrO2, on the structural properties of their nanocomposites with high-density polyethylene (HDPE). The composite films were prepared by melt-blending with a filler content that varied from 1% to 20% v/v. The composites were characterized by small- and wide-angle x-ray scattering (SAXS and WAXS), small-angle neutron scattering (SANS), Raman spectroscopy, differential scanning calorimetry (DSC), and scanning electron microscopy (SEM). For both fillers, the nanoaggregates were evenly distributed in the polymer matrix and their initial state in the powders determined their surface roughness and fractal character. In the case of the nano-ZrO2 filler, the lamellar thickness and crystallinity degree remain unchanged over a broad range of filler concentrations. SANS and SEM investigation showed poor interfacial adhesion and the presence of voids in the interfacial region. Temperature-programmed SANS investigations showed that at elevated temperatures, these voids become filled due to the flipping motions of polymer chains. The effect was accompanied by a partial aggregation of the filler. For nano-SiO2 filler, the lamellar thickness and the degree of crystallinity increased with increasing the filler loading. SAXS measurements show that the ordering of the lamellae is disrupted even at a filler content of only a few percent. SEM images confirmed good interfacial adhesion and integrity of the SiO2/HDPE composite. This markedly different impact of both fillers on the composite structure is discussed in terms of nanoparticle surface properties and their affinity to the HDPE matrix.

Cotton Textile/Iron Oxide Nanozyme Composites with Peroxidase-like Activity: Preparation, Characterization, and Application.

At present, both native and immobilized nanoparticles are of great importance in many areas of science and technology. In this paper, we have studied magnetic iron oxide nanoparticles and their aggregates bound on woven cotton textiles employing two simple modification procedures. One modification was based on the treatment of textiles with perchloric-acid-stabilized magnetic fluid diluted with methanol followed by drying. The second procedure was based on the microwave-assisted conversion of ferrous sulfate at high pH followed by drying. The structure and functional properties of these modified textiles were analyzed in detail. Scanning electron microscopy of native and modified textiles clearly showed the presence of iron oxide nanoparticles on the surface of the modified cotton fibers. All of the modified textile materials exhibited light to dark brown color depending on the amount of the bound iron oxide particles. Magnetic measurements showed that the saturation magnetization values reflect the amount of magnetic nanoparticles present in the modified textiles. Small-angle X-ray and neutron scattering measurements were conducted for the detailed structural characterization at the nanoscale of both the native and magnetically modified textiles, and different structural organization of nanoparticles in the two kinds of textile samples were concluded. The textile-bound iron oxide particles exhibited peroxidase-like activity when the N,N-diethyl-p-phenylenediamine sulfate salt was used as a substrate; this nanozyme activity enabled rapid decolorization of crystal violet in the presence of hydrogen peroxide. The deposition of a sufficient amount of iron oxide particles on textiles enabled their simple magnetic separation from large volumes of solutions; if necessary, the magnetic response of the modified textiles can be simply increased by incorporation of a piece of magnetic iron wire. The simplicity of the immobilized nanozyme preparation and the low cost of all the precursors enable its widespread application, such as decolorization and degradation of selected organic dyes and other important pollutants. Other types of textile-bound nanozymes can be prepared and used as low-cost catalysts for a variety of applications.

Comparison of Structure and Adsorption Properties of Mesoporous Silica Functionalized with Aminopropyl Groups by the Co-Condensation and the Post Grafting Methods.

The adsorptive potential has been evaluated for the aminopropyl functionalized mesoporous silica materials obtained by co-condensation and post grafting methods. Nitrogen sorption, small angle neutron and X-ray scattering (SANS and SAXS) demonstrated high surface area and well-ordered hexagonal pore structure suitable for applications as adsorbents of metals from waste waters. A comparison of Cr(VI) adsorption properties of the materials prepared by different functionalization methods has been performed. The obtained results demonstrated the adsorption capacity due to the affinity of the chromium ions to the amino groups, and showed that co-condensation of tetraethoxysilane (TEOS) and 3-aminopropyl triethoxysilane (APTES) resulted in higher metal sorption capacity of the materials compared to post-synthesis grafting of aminopropyl groups onto the mesoporous silica particles.

Fluorination of Diamond Nanoparticles in Slow Neutron Reflectors Does Not Destroy Their Crystalline Cores and Clustering While Decreasing Neutron Losses.

If the wavelength of radiation and the size of inhomogeneities in the medium are approximately equal, the radiation might be intensively scattered in the medium and reflected from its surface. Such efficient nanomaterial reflectors are of great scientific and technological interest. In previous works, we demonstrated a significant improvement in the efficiency of reflection of slow neutrons from a powder of diamond nanoparticles by replacing hydrogen located on the surface of nanoparticles with fluorine and removing the residual sp2 amorphous shells of nanoparticles via the fluorination process. In this paper, we study the mechanism of this improvement using a set of complementary experimental techniques. To analyze the data on a small-angle scattering of neutrons and X-rays in powders of diamond nanoparticles, we have developed a model of discrete-size diamond nanospheres. Our results show that fluorination does not destroy either the crystalline cores of nanoparticles or their clustering in the scale range of 0.6-200 nm. This observation implies that it does not significantly affect the neutron scattering properties of the powder. We conclude that the overall increase in reflectivity from the fluorinated nanodiamond powder is primarily due to the large reduction of neutron losses in the powder caused by the removal of hydrogen contaminations.

Fullerenes as an Effective Amyloid Fibrils Disaggregating Nanomaterial.

Nowadays, determining the disassembly mechanism of amyloids under nanomaterials action is a crucial issue for their successful future use in therapy of neurodegenerative and overall amyloid-related diseases. In this study, the antiamyloid disassembly activity of fullerenes C60 and C70 dispersed in 1-methyl-2-pyrrolidinone (NMP) toward amyloid fibrils preformed from lysozyme and insulin was investigated using a combination of different experimental techniques. Thioflavin T fluorescence assay and atomic force microscopy were applied for monitoring of disaggregation activity of fullerenes. It was demonstrated that both types of fullerene-based complexes are very effective in disassembling preformed fibrils, and characterized by the low apparent half-maximal disaggregation concentration (DC50) in the range of ∼22-30 µg mL-1. Small-angle neutron scattering was employed to monitor the different stages of the disassembly process with respect to the size and morphology of the aggregates. Based on the obtained results, a possible disassembly mechanism for amyloid fibrils interacting with fullerene/NMP complexes was proposed. The study is a principal step in understanding of the fullerenes destruction mechanism of the protein amyloids, as well as providing valuable information on how macromolecules can be engineered to disassemble unwanted amyloid aggregates by different mechanisms.

Solubilisation of model membrane by DDAO surfactant - partitioning, permeabilisation and liposome-micelle transition.

Solubilisation of model membranes of dioleoylphosphatidylcholine (DOPC) and DOPCcholesterol (CHOL) induced by surfactant N,N-dimethyl-1-dodecanamine-N-oxide (DDAO) was studied. At the maintained pH ~ 7.5, the DDAO molecules are in their neutral state with respect to the pK ~ 5. Pore formation in lipid bilayer was studied by fluorescence probe leakage method. The changes in the size of lipid aggregates upon increasing DDAO concentration were followed turbidimetrically. Effective ratio Re at different steps of the solubilisation process was determined. The molar partition coefficient of DDAO in case of the DOPC membrane is Kp = 2262 ± 379, for DOPC-CHOL membrane Kp = 2092 ± 594. Within the experimental error, the partition coefficient, as well as effective ratios Re, are not considerably influenced when one third of DOPC molecules is substituted with CHOL (DOPC:CHOL = 2:1). Constituents of buffer (50 mmol/dm3 PBS, 150 mmol/dm3 NaCl) caused aggregation of DOPC and DOPC-CHOL unilamellar liposomes at zero and low DDAO concentration, as was shown by SANS, turbidimetry and DIC microscopy. After solubilisation of bilayer structures by surfactant, mixed DOPC-DDAO and DOPC-CHOL-DDAO micelles with the shape of cylinders with elliptical cross section were detected.

Structural changes introduced by cholesterol and melatonin to the model membranes mimicking preclinical conformational diseases.

The structure and dynamics of membranes depend on many external and internal factors that in turn determine their biological functions. One of the widely accepted and studied characteristics of biomembranes is their fluidity. We research a simple system with variable fluidity tweakable via its composition. The addition of cholesterol is employed to increase the order of lipid chains, thus decreasing the membrane fluidity, while melatonin is shown to elevate the chain disorder, thus also the membrane fluidity. We utilize the densitometric measurements to show a shift of studied systems closer or further from the gel-to-fluid phase transition. The structural changes represented by changes to membrane thickness are evaluated from small angle neutron scattering. Finally, we look at the ability of the two additives to control the interactions between membrane and amyloid-beta peptides. Our results suggest that fluidizing effect of melatonin can promote an insertion of peptide within the membrane interior. Intriguingly, the latter structure relates possibly to an Alzheimer's disease preventing mechanism postulated in the case of melatonin.

Size and distribution of the iron oxide nanoparticles in SBA-15 nanoporous silica via SANS study.

Structural characteristics of nanocomposite series consisting of iron oxide nanoparticles (NPs) embedded in the regular pores of amorphous silica matrix (SBA-15) were investigated by means of small angle neutron scattering (SANS). By virtue of unique neutron properties, insight into the inner structure and matter organization of this kind of systems was facilitated for the first time. Based on rigorous experimental support, fundamental model describing the neutron scattering intensity distribution was proposed by assuming general composite structural features. Model application to SANS data confirmed the presence of iron oxide NPs in the body of examined matrices, providing additional information on their shape, concentration and size distribution. Scattering superposition principle employed in the model conception allows for tailoring its fundamental characteristics, and renders it a potent and versatile tool for a wide range of applications.

Small-angle neutron and X-ray scattering analysis of the supramolecular organization of rhodopsin in photoreceptor membrane.

The supramolecular organization of the visual pigment rhodopsin in the photoreceptor membrane remains contentious. Specifically, whether this G protein-coupled receptor functions as a monomer or dimer remains unknown, as does the presence or absence of ordered packing of rhodopsin molecules in the photoreceptor membrane. Completely opposite opinions have been expressed on both issues. Herein, using small-angle neutron and X-ray scattering approaches, we performed a comparative analysis of the structural characteristics of the photoreceptor membrane samples in buffer, both in the outer segment of photoreceptor cells, and in the free photoreceptor disks. The average distance between the centers of two neighboring rhodopsin molecules was found to be ~5.8 nm in both cases. The results indicate an unusually high packing density of rhodopsin molecules in the photoreceptor membrane, but molecules appear to be randomly distributed in the membrane without any regular ordering.