Tandem X-ray absorption spectroscopy and scattering for in situ time-resolved monitoring of gold nanoparticle mechanosynthesis.

Current time-resolved in situ approaches limit the scope of mechanochemical investigations possible. Here we develop a new, general approach to simultaneously follow the evolution of bulk atomic and electronic structure during a mechanochemical synthesis. This is achieved by coupling two complementary synchrotron-based X-ray methods: X-ray absorption spectroscopy (XAS) and X-ray diffraction. We apply this method to investigate the bottom-up mechanosynthesis of technologically important Au micro and nanoparticles in the presence of three different reducing agents, hydroquinone, sodium citrate, and NaBH4. Moreover, we show how XAS offers new insight into the early stage generation of growth species (e.g. monomers and clusters), which lead to the subsequent formation of nanoparticles. These processes are beyond the detection capabilities of diffraction methods. This combined X-ray approach paves the way to new directions in mechanochemical research of advanced electronic materials.

Advances in Nickel Nanoparticle Synthesis via Oleylamine Route.

Nickel nanoparticles are an active research area due to their multiple applications as catalysts in different processes. A variety of preparation techniques have been reported for the synthesis of these nanoparticles, including solvothermal, microwave-assisted, and emulsion techniques. The well-studied solvothermal oleylamine synthesis route comes with the drawback of needing standard air-free techniques and often space-consuming glassware. Here, we present a facile and straightforward synthesis method for size-controlled highly monodisperse nickel nanoparticles avoiding the use of, e.g., Schlenk techniques and space-consuming labware. The nanoparticles produced by this novel synthetic route were investigated using small-angle X-ray scattering, transmission electron microscopy, X-ray diffraction, and X-ray spectroscopy. The nanoparticles were in a size range of 4‒16 nm, show high sphericity, no oxidation, and no agglomeration after synthesis.

Thermally highly stable amorphous zinc phosphate intermediates during the formation of zinc phosphate hydrate.

The mechanisms by which amorphous intermediates transform into crystalline materials are still poorly understood. Here we attempt to illuminate the formation of an amorphous precursor by investigating the crystallization process of zinc phosphate hydrate. This work shows that amorphous zinc phosphate (AZP) nanoparticles precipitate from aqueous solutions prior to the crystalline hopeite phase at low concentrations and in the absence of additives at room temperature. AZP nanoparticles are thermally stable against crystallization even at 400 °C (resulting in a high temperature AZP), but they crystallize rapidly in the presence of water if the reaction is not interrupted. X-ray powder diffraction with high-energy synchrotron radiation, scanning and transmission electron microscopy, selected area electron diffraction, and small-angle X-ray scattering showed the particle size (≈20 nm) and confirmed the noncrystallinity of the nanoparticle intermediates. Energy dispersive X-ray, infrared, and Raman spectroscopy, inductively coupled plasma mass spectrometry, and optical emission spectrometry as well as thermal analysis were used for further compositional characterization of the as synthesized nanomaterial. (1)H solid-state NMR allowed the quantification of the hydrogen content, while an analysis of (31)P{(1)H} C rotational echo double resonance spectra permitted a dynamic and structural analysis of the crystallization pathway to hopeite.

Processing nanoparticles with A4F-SAXS for toxicological studies: Iron oxide in cell-based assays.

Nanoparticles are not typically ready-to-use for in vitro cell culture assays. Prior to their use in assays, powder samples containing nanoparticles must be dispersed, de-agglomerated, fractionated by size, and characterized with respect to size and size distribution. For this purpose we report exemplarily on polyphosphate-stabilized iron oxide nanoparticles in aqueous suspension. Fractionation and online particle size analysis was performed in a time-saving procedure lasting 50 min by combining asymmetrical flow field-flow fractionation (A4F) and small-angle X-ray scattering (SAXS). Narrowly distributed nanoparticle fractions with radii of gyration (R(g)) from 7 to 21 nm were obtained from polydisperse samples. The A4F-SAXS combination is introduced for the preparation of well-characterized sample fractions originating from a highly polydisperse system as typically found in engineered nanoparticles. A4F-SAXS processed particles are ready-to-use for toxicological studies. The results of preliminary tests of the effects of fractionated iron oxide nanoparticles with a R(g) of 15 nm on a human colon model cell line are reported.

The size distribution of 'gold standard' nanoparticles.

The spherical gold nanoparticle reference materials RM 8011, RM 8012, and RM 8013, with a nominal radius of 5, 15, and 30 nm, respectively, have been available since 2008 from NIST. These materials are recommended as standards for nanoparticle size measurements and for the study of the biological effects of nanoparticles, e.g., in pre-clinical biomedical research. We report on determination of the size distributions of these gold nanoparticles using different small-angle X-ray scattering (SAXS) instruments. Measurements with a classical Kratky type SAXS instrument are compared with a synchrotron SAXS technique. Samples were investigated in situ, positioned in capillaries and in levitated droplets. The number-weighted size distributions were determined applying model scattering functions based on (a) Gaussian, (b) log-normal, and (c) Schulz distributions. The mean radii are 4.36 +/- 0.04 nm (RM 8011), 12.20 +/- 0.03 nm (RM 8012), and 25.74 +/- 0.27 nm (RM 8013). Low polydispersities, defined as relative width of the distributions, were detected with values of 0.067 +/- 0.006 (RM 8011), 0.103 +/- 0.003, (RM 8012), and 0.10 +/- 0.01 (RM 8013). The results are in agreement with integral values determined from classical evaluation procedures, such as the radius of gyration (Guinier) and particle volume (Kratky). No indications of particle aggregation and particle interactions--repulsive or attractive--were found. We recommend SAXS as a standard method for a fast and precise determination of size distributions of nanoparticles.

Online coupling of field-flow fractionation with SAXS and DLS for polymer analysis.

We report on a hyphenated polymer analysis method consisting of asymmetrical flow field-flow fractionation (A4F) coupled online with small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS). A mixture of six poly(styrene sulfonate)s with molar masses in the range of 6.5 × 103 to 1.0 × 106 g mol-1 was used as a model system for polyelectrolytes in aqueous solutions with a broad molar mass distribution. A complete polymer separation and analysis was performed in 60 min. Detailed information for all polymer fractions are available on i) the radii of gyration, which were determined from the SAXS data interpretation in terms of the Debye model (Gaussian chains), and ii) the diffusion coefficients (from DLS). We recommend using the A4F-SAXS-DLS coupling as a possible new reference method for the detailed analysis of complex polymer mixtures. Advantages of the use of SAXS are seen in comparison to static light scattering for polymers with radii of gyration smaller then 15 nm, for which only SAXS produces precise analytical results on the size of the polymers in solution.

1.55 A structure of the ectoine binding protein TeaA of the osmoregulated TRAP-transporter TeaABC from Halomonas elongata.

TeaABC from the moderate halophilic bacterium Halomonas elongata belongs to the tripartite ATP-independent periplasmic transporters (TRAP-T), a family of secondary transporters functioning in conjunction with periplasmic substrate binding proteins. TeaABC facilitates the uptake of the compatible solutes ectoine and hydroxyectoine that are accumulated in the cytoplasm under hyperosmotic stress to protect the cell from dehydration. TeaABC is the only known TRAP-T activated by osmotic stress. Currently, our knowledge on the osmoregulated compatible solute transporter is limited to ABC transporters or conventional secondary transporters. Therefore, this study presents the first detailed analysis of the molecular mechanisms underlying substrate recognition of the substrate binding protein of an osmoregulated TRAP-T. In the present study we were able to demonstrate by isothermal titration calorimetry measurements that TeaA is a high-affinity ectoine binding protein ( K d = 0.19 microM) that also has a significant but somewhat lower affinity to hydroxyectoine ( K d = 3.8 microM). Furthermore, we present the structure of TeaA in complex with ectoine at a resolution of 1.55 A and hydroxyectoine at a resolution of 1.80 A. Analysis of the TeaA binding pocket and comparison of its structure to other compatible solute binding proteins from ABC transporters reveal common principles in compatible solute binding but also significant differences like the solvent-mediated specific binding of ectoine to TeaA.

Agglomeration of proteins in acoustically levitated droplets.

An ultrasonic trap (acoustic levitator) was used as an analytical tool to allow container-free handling of proteins in small sample volumes. This trap was combined for the first time with synchrotron small-angle X-ray scattering (SAXS) for structure analysis of biological macromolecules in a solution. The microfocus beamline at BESSY was used as a source of intense X-ray radiation. Apoferritin (APO) was used as a model protein, and its aggregation behavior in a levitator was followed from a diluted solution to the solid state. Different stages of APO agglomeration were observed without solid container walls, which may influence aggregation behavior and produce a parasitic scattering background. Starting with a volume of 5 microL we analyzed the concentration dependence of APO structure factors in the range from 5 to 1,200 mg/mL (solid protein). The solution was stirred automatically due to convection inside the droplet caused by the ultrasonic field. SAXS data recording of APO was performed in time intervals of 60 s during an aggregation experiment of 30 to 60 min.

Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.

Bacterial cold shock proteins (CSPs) regulate cellular adaptation to cold stress. Functions ascribed to CSP include roles as RNA chaperones and in transcription antitermination. We present the crystal structure of the Bacillus caldolyticus CSP (Bc-Csp) in complex with hexathymidine (dT(6)) at a resolution of 1.29 A. Bound to dT(6), crystalline Bc-Csp forms a domain-swapped dimer in which beta strands 1-3 associate with strands 4 and 5 from the other subunit to form a closed beta barrel and vice versa. The globular units of dimeric Bc-Csp closely resemble the well-known structure of monomeric CSP. Structural reorganization from the monomer to the domain-swapped dimer involves a strictly localized change in the peptide bond linking Glu36 and Gly37 of Bc-Csp. Similar structural reorganizations have not been found in any other CSP or oligonucleotide/oligosaccharide-binding fold structures. Each dT(6) ligand is bound to one globular unit of Bc-Csp via an amphipathic protein surface. Individual binding subsites interact with the DNA bases through stacking and hydrogen bonding. The sugar-phosphate backbone remains solvent exposed. Based on crystallographic and biochemical studies of deoxyoligonucleotide binding to CSP, we suggest a common mode of binding of single-stranded heptanucleotide motifs to proteins containing cold shock domains, including the eukaryotic Y-box factors.

H-bonding-directed self-assembly of synthetic copolymers containing nucleobases: organization and colloidal fusion in a noncompetitive solvent.

The self-organization of random copolymers composed of a nucleobase monomer (either 1-(4-vinylbenzyl)thymine or 9-(4-vinylbenzyl)adenine) and dodecyl methacrylate (DMA) was studied in dilute chloroform solutions. The balance between the molar fractions of the nucleobase monomer (leading to intermolecular H-bonding) and DMA (soluble moiety in chloroform) in the polymer chains was found to be the parameter that principally influences the self-organization. DMA-rich copolymers are molecularly soluble in chloroform, whereas nucleobase-rich copolymers are insoluble in this solvent. Copolymers possessing an equimolar comonomer composition self-assemble into micrometer-sized particles physically cross-linked by intermolecular H-bonds (either thymine-thymine or adenine-adenine interactions, depending on the studied copolymer). Nevertheless, when mixed together, thymine- and adenine-based colloids fuse into thermodynamically stable microspheres cross linked by adenine-thymine interactions.

T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.

Bacterial cold shock proteins (CSPs) are involved in cellular adaptation to cold stress. They bind to single-stranded nucleic acids with a KD value in the micro- to nanomolar range. Here we present the structure of the Bacillus subtilis CspB (Bs-CspB) in complex with hexathymidine (dT6) at a resolution of 1.78 A. Bs-CspB binds to dT6 with nanomolar affinity via an amphipathic interface on the protein surface. Individual binding subsites interact with single nucleobases through stacking interactions and hydrogen bonding. The sugar-phosphate backbone and the methyl groups of the thymine nucleobases remain solvent exposed and are not contacted by protein groups. Fluorescence titration experiments monitoring the binding of oligopyrimidines to Bs-CspB reveal binding preferences at individual subsites and allow the design of an optimised heptapyrimidine ligand, which is bound with sub-nanomolar affinity. This study reveals the stoichiometry and sequence determinants of the binding of single-stranded nucleic acids to a preformed site on Bs-CspB and thus provides the structural basis of the RNA chaperone and transcription antitermination activities of the CSP.

V-shaped crystalline structures of di-n-alkyl esters of phosphoric acid.

We prepared crystals of di-n-alkyl esters of phosphoric acid with chain lengths of n = 10, 12, 14, 16, and 18. These were characterized by single-crystal X-ray analysis and differential scanning calorimetry (DSC). It was found that the alkyl chains are in an extended all-trans conformation and aligned close to perpendicular, forming V-shaped molecules. This is in strong contrast to the typical arrangement of the alkyl chains of phospholipids where the two alkyl chains are arranged parallel in the same direction (e.g., tuning fork configuration in bilayers). Additionally, it was found that the arrangement of the V-shaped molecules of the di-n-alkyl esters in neighboring stacks of the lamellar crystals is antiparallel for short chain lengths (n = 10 and 12) and parallel for the longer (n = 14 and 16). DSC reveals that the melting of the crystals increases systematically with increasing chain lengths from 48 to 82 degrees C. The contribution of each methylene group to the melting enthalpy (70-133 kJ/mol) is independent of the chain length (3.9 kJ per mol CH2).

Crystal structure of NblA from Anabaena sp. PCC 7120, a small protein playing a key role in phycobilisome degradation.

Cyanobacterial light-harvesting complexes, the phycobilisomes, are proteolytically degraded when the organisms are starved for combined nitrogen, a process referred to as chlorosis or bleaching. Gene nblA, present in all phycobilisome-containing organisms, encodes a protein of about 7 kDa that plays a key role in phycobilisome degradation. The mode of action of NblA in this degradation process is poorly understood. Here we presented the 1.8-A crystal structure of NblA from Anabaena sp. PCC 7120. In the crystal, NblA is present as a four-helix bundle formed by dimers, the basic structural units. By using pull-down assays with immobilized NblA and peptide scanning, we showed that NblA specifically binds to the alpha-subunits of phycocyanin and phycoerythrocyanin, the main building blocks of the phycobilisome rod structure. By site-directed mutagenesis, we identified amino acid residues in NblA that are involved in phycobilisome binding. The results provided evidence that NblA is directly involved in phycobilisome degradation, and the results allowed us to present a model that gives insight into the interaction of this small protein with the phycobilisomes.

Single-stranded DNA bound to bacterial cold-shock proteins: preliminary crystallographic and Raman analysis.

The cold-shock response has been described for several bacterial species. It is characterized by distinct changes in intracellular protein patterns whereby a set of cold-shock-inducible proteins become abundant. The major cold-shock proteins of Bacillus subtilis (Bs-CspB) and Bacillus caldolyticus (Bc-Csp) are small oligonucleotide/oligosaccharide-binding (OB) fold proteins that have been described as binding single-stranded nucleic acids. Bs-CspB (Mr = 7365) and Bc-Csp (Mr = 7333) were crystallized in the presence of the deoxyhexanucleotide (dT)6. Crystals of (dT)6 with Bs-CspB grew in the orthorhombic space group C222(1), with unit-cell parameters a = 49.0, b = 53.2, c = 77.0 A. Crystals with Bc-Csp grew in the primitive orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 74.3, b = 64.9, c = 31.2 A. These crystals diffract to maximal resolutions of 1.78 and 1.29 A, respectively. The presence of protein and DNA in the crystals was demonstrated by Raman spectroscopy.

Characterization and analysis of posttranslational modifications of the human large cytoplasmic ribosomal subunit proteins by mass spectrometry and Edman sequencing.

The 60S ribosomal proteins were isolated from ribosomes of human placenta and separated by reversed phase HPLC. The fractions obtained were subjected to trypsin and Glu-C digestion and analyzed by mass fingerprinting (MALDI-TOF), MS/MS (ESI), and Edman sequencing. Forty-six large subunit proteins were found, 22 of which showed masses in accordance with the SwissProt database (June 2002) masses (proteins L6, L7, L9, L13, L15, L17, L18, L21, L22, L24, L26, L27, L30, L32, L34, L35, L36, L37, L37A, L38, L39, L41). Eleven (proteins L7, L10A, L11, L12, L13A, L23, L23A, L27A, L28, L29, and P0) resulted in mass changes that are consistent with N-terminal loss of methionine, acetylation, internal methylation, or hydroxylation. A loss of methionine without acetylation was found for protein L8 and L17. For nine proteins (L3, L4, L5, L7A, L10, L14, L19, L31, and L40), the molecular masses could not be determined. Proteins P1 and protein L3-like were not identified by the methods applied.