Supramolecular Structure of TTBC J‑Aggregates in Solution and on Surface

The aggregation behavior of cationic 5,5′,6,6′-tetrachloro-1,1′,3,3′-tetraethylbenzimidacarbocyanine with chloride (TTBC-Cl) or iodide counterions (TTBC-I) in aqueous solution is investigated by absorption, linear dichroism, and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). TTBC-Cl is found to form J-aggregates with a classical Davydov-split absorption band (type I spectrum) even under different preparation conditions. These aggregates remain stable for months. Unlike the chloride salt, the iodide salt TTBC-I forms two different types of J-aggregates depending on the pH of the aqueous solution. The TTBC-I aggregates prepared in pure water (pH = 6) are characterized by a single redshifted absorption band (type III spectrum), whereas those prepared in alkaline solution at pH = 13 show a typical Davydov-split (type I) absorption band. Despite differences in counterions, preparation method, stability, and spectroscopic behavior, cryo-TEM reveals an identical tubular architecture for all these J-aggregates. Among the new structure models discussed here is a cylindrical brickwork layer of dye molecules for single-banded J-aggregates (type III). For Davydov-split aggregates (type I), a molecular herringbone-like pattern is proposed instead. Moreover, absorption spectra have revealed an additional single redshifted absorption band (type II spectrum) that is assigned to a surface aggregate and is induced by a specific interaction of the dye cation with the negatively charged cuvette wall. AFM measurements of analogous preparations on negatively charged mica surfaces have supported this interpretation and revealed the formation of monolayered sheet structures

H‑Aggregates of an Indocyanine Cy5 Dye: Transition from Strong to Weak Molecular Coupling

The aggregation behavior of an Indocyanine Cy5 dye (2-[5-[1,1-dimethyl-3-(4-sulfobutyl)-1,3-dihydro-benzo­[e]­indol-2-ylidene]-penta-1,3-dienyl]-1,1-dimethyl-3-(4-sulfobutyl)-1<i>H</i>-benzo­[e]­indolium hydroxide, inner salt, sodium salt) in aqueous solution is investigated using absorption and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM). The dye concentration is varied within a broad range from ∼1 μM to ∼10 mM. At moderate concentrations, typical H-aggregates are formed. After longer storage time, the absorption spectra of these solutions change dramatically. The characteristic blue-shifted absorption band at around 600 nm becomes replaced by a three-banded absorption spectrum, which spreads over a wide wavelength range of ∼600 up to 800 nm. However, at the highest dye concentration and in the presence of ∼(10 to 30) mM NaCl, the three-banded spectrum is observed directly after preparation. The spectroscopic features can be ascribed to a structural transformation of strongly to weakly coupled H-type aggregates. The transformation is promoted by an increase of the ionic strength. Cryo-TEM data reveal that the weakly coupled H′-aggregates are organized in well-ordered, extended monolayer sheets, whereas the strongly coupled H-aggregates appear to consist of particles of only a few nanometers in size

Effect of Cultivar and Cultivation Year on the Metabolite Profile of Onion Bulbs (<i>Allium cepa</i> L.)

This study investigated the variation of metabolite profiles of onion bulbs (<i>Allium cepa</i> L.) depending on genetic and environmental factors. Nine onion cultivars (“Corrado”, “Cupido”, “Forum”, “Hytech”, “Picador”, “Redlight”, “Snowpack”, “Stardust”, “Sturon”) with different scale color and dry matter content were grown in a two-year field trial. Using a recently established metabolite profiling approach based on liquid chromatography-coupled electrospray ionization quadrupole time-of-flight mass spectrometry, 106 polar and semipolar metabolites which belong to compound classes determining nutritional, sensory, and technological quality of onion bulbs such as saccharides, flavonoids, S-substitued cysteine conjugates, amino acids, and derived γ-glutamyl peptides were relatively quantitated in parallel. Statistical analyses of the obtained data indicated that depending on the compound class genetic and environmental factors differently contributed to variation of metabolite levels. For saccharides and flavonoids the genetic factor was the major source of variation, whereas for cysteine sulfoxides, amino acids, and peptides both genetic and environmental factors had a significant impact on corresponding metabolite levels

Gold Nanoparticle Inclusion into Protein Nanotube as a Layered Wall Component

We describe the synthesis, structure, and catalytic activity of human serum albumin (HSA) nanotubes (NTs) including gold nanoparticles (AuNPs) as a layered wall component. The NTs were fabricated as an alternating layer-by-layer assembly of AuNP and HSA admixture (a negatively charged part) and poly-l-arginine (PLA, a positively charged part) into a track-etched polycarbonate membrane (400 nm pore diameter) with subsequent dissolution of the template. SEM images showed the formation of uniform hollow cylinders of (PLA/AuNP-HSA)₃ with a 426 ± 12 nm outer diameter and 65 ± 7 nm wall thickness. Transmission electron microscopy and energy dispersive X-ray measurements revealed high loading of AuNPs in the tubular wall. HSAs bind strongly onto the individual AuNP (<i>K</i> = 1.25 × 10⁹ M^–1), generating a core–shell AuNP-HSA corona, which is the requirement of the robust NT formation. Calcination of the (PLA/AuNP-HSA)₃ NTs at 500 °C under air yielded red solid NTs composed of thermally fused AuNPs. From the mass decrease by heat treatment, we calculated the weight of the organic components (PLA and HSA) and thereby constructed a six-layer model of the tube. The (PLA/AuNP-HSA)₃ NTs serve as a heterogeneous catalyst for reduction of 4-nitrophenol with sodium borohydrate. Furthermore, implantation of the stiff (PLA/AuNP-HSA)₃ NTs vertically onto glass plate produced uniformly cylindrical tube arrays

An UPLC-MS/MS Method for the Simultaneous Identification and Quantitation of Cell Wall Phenolics in Brassica napus Seeds

The seed residues left after pressing of rapeseed oil are rich in proteins and could be used for human nutrition and animal feeding. These press cakes contain, however, antinutritives, with fiber being the most abundant one. The analysis of fiber phenolic component (localized to seed coat cell walls) is, therefore, important in breeding and food quality control. However, correct structure and content assignments of cell wall-bound phenolics are challenging due to their low stability during sample preparation. Here, a novel LC-MS/MS-based method for the simultaneous identification and quantitation of 66 cell wall-bound phenolics and their derivatives is described. The method was internally standardized, corrected for degradation effects during sample preparation, and cross-validated with a well-established UV-based procedure. This approach was successfully applied to the analysis of cell wall phenolic patterns in different <i>B. napus</i> cultivars and proved to be suitable for marker compound search as well as assay development

CAMERA: An Integrated Strategy for Compound Spectra Extraction and Annotation of Liquid Chromatography/Mass Spectrometry Data Sets

Liquid chromatography coupled to mass spectrometry is routinely used for metabolomics experiments. In contrast to the fairly routine and automated data acquisition steps, subsequent compound annotation and identification require extensive manual analysis and thus form a major bottleneck in data interpretation. Here we present CAMERA, a Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data. To evaluate the algorithms, we compared the annotation of CAMERA against a manually defined annotation for a mixture of known compounds spiked into a complex matrix at different concentrations. CAMERA successfully extracted accurate masses for 89.7% and 90.3% of the annotatable compounds in positive and negative ion modes, respectively. Furthermore, we present a novel annotation approach that combines spectral information of data acquired in opposite ion modes to further improve the annotation rate. We demonstrate the utility of CAMERA in two different, easily adoptable plant metabolomics experiments, where the application of CAMERA drastically reduced the amount of manual analysis

Structural Insights into a Hemoglobin–Albumin Cluster in Aqueous Medium

A hemoglobin (Hb) wrapped covalently by three human serum albumins (HSAs) is a triangular protein cluster designed as an artificial O₂-carrier and red blood cell substitute. We report the structural insights into this Hb-HSA₃ cluster in aqueous medium revealed by 3D reconstruction based on cryogenic transmission electron microscopy (cryo-TEM) data and small-angle X-ray scattering (SAXS) measurements. Cryo-TEM observations showed individual particles with approximately 15 nm diameter in the vitrified ice layer. Subsequent image processing and 3D reconstruction proved the expected spatial arrangements of an Hb in the center and three HSAs at the periphery. SAXS measurements demonstrated the monodispersity of the Hb-HSA₃ cluster having a molecular mass of 270 kDa. The pair-distance distribution function suggested the existence of oblate-like particles with a maximum dimeter of ∼17 nm. The supramolecular 3D structure reconstructed from the SAXS intensity using an <i>ab initio</i> procedure was similar to that obtained from cryo-TEM data

Covalent Core–Shell Architecture of Hemoglobin and Human Serum Albumin as an Artificial O₂ Carrier

Covalent core–shell structured protein clusters of hemoglobin (Hb) and human serum albumin (HSA) (Hb<b>X</b>-HSA_<i>m</i>) (<i>m</i> = 2, 3) with novel physiological properties were generated by linkage of Hb surface lysins to HSA cysteine-34 via an α-succinimidyl-ε-maleimide cross-linker (<b>X</b>: <b>1</b> or <b>2</b>). The isoelectric points of Hb<b>X</b>-HSA_<i>m</i> (p<i>I</i> = 5.0–5.2) were markedly lower than that of Hb and almost identical to that of HSA. AFM and TEM measurements revealed a triangular Hb<b>1</b>-HSA₃ cluster in aqueous medium. The complete 3D structure of Hb<b>1</b>-HSA₃ based on TEM data was reconstructed, revealing two possible conformer variants. All Hb<b>X</b>-HSA_<i>m</i> clusters showed a moderately higher O₂ affinity than the native Hb. Furthermore, the exterior HSA units possess a remarkable ability to bind lumiflavin (LF). The addition of NADH to an aqueous solution of the met-Hb<b>2</b>-(HSA-LF)₃ cluster reduced the inactive ferric Hb center to the functional ferrous Hb. This O₂-carrying hemoprotein cluster with strongly negative surface net charge, high O₂ affinity, and NADH-dependent reductase unit can support a new generation of molecular architecture for red blood cell substitutes

Tandem Coordination, Ring-Opening, Hyperbranched Polymerization for the Synthesis of Water-Soluble Core–Shell Unimolecular Transporters

A water-soluble molecular transporter with a dendritic core–shell nanostructure has been prepared by a tandem coordination, ring-opening, hyperbranched polymerization process. Consisting of hydrophilic hyperbranched polyglycerol shell grafted from hydrophobic dendritic polyethylene core, the transporter has a molecular weight of 951 kg/mol and a hydrodynamic diameter of 17.5 ± 0.9 nm, as determined by static and dynamic light scattering, respectively. Based on evidence from fluorescence spectroscopy, light scattering, and electron microscopy, the core–shell copolymer transports the hydrophobic guests pyrene and Nile red by a unimolecular transport mechanism. Furthermore, it was shown that the core–shell copolymer effectively transports the hydrophobic dye Nile red into living cells under extremely high and biologically relevant dilution conditions, which is in sharp contrast to a small molecule amphiphile. These results suggest potential applicability of such core–shell molecular transporters in the administration of poorly water-soluble drugs

Multivalency at Interfaces: Supramolecular Carbohydrate-Functionalized Graphene Derivatives for Bacterial Capture, Release, and Disinfection

A supramolecular carbohydrate-functionalized two-dimensional (2D) surface was designed and synthesized by decorating thermally reduced graphene sheets with multivalent sugar ligands. The formation of host–guest inclusions on the carbon surface provides a versatile strategy, not only to increase the intrinsic water solubility of graphene-based materials, but more importantly to let the desired biofunctional binding groups bind to the surface. Combining the vital recognition role of carbohydrates and the unique 2D large flexible surface area of the graphene sheets, the addition of multivalent sugar ligands makes the resulting carbon material an excellent platform for selectively wrapping and agglutinating <i>Escherichia coli</i> <i>(E. coli</i>)<i>.</i> By taking advantage of the responsive property of supramolecular interactions, the captured bacteria can then be partially released by adding a competitive guest. Compared to previously reported scaffolds, the unique thermal IR-absorption properties of graphene derivatives provide a facile method to kill the captured bacteria by IR-laser irradiation of the captured graphene–sugar–<i>E. coli</i> complex