Synthesis and characterization of TEMPO-oxidized peptide-cellulose conjugate biosensors for detecting human neutrophil elastase

Cellulose - Here we describe the synthesis and characterization of a peptide-cellulose conjugate biosensor based on TEMPO-oxidized nanofibrillated cellulose (tNFC) for detecting elevated levels of...     

A high-performance liquid chromatography-tandem mass spectrometry method for quantitation of nitrogen-containing intracellular metabolites

A comprehensive method of quantifying intracellular metabolite concentrations would be a valuable addition to the arsenal of tools for holistic biochemical studies. Here, we describe a step toward the development of such method: a quantitative assay for 90 nitrogen-containing cellular metabolites. The assay involves reverse-phase high-performance liquid chromatography separation followed by electrospray ionization and detection of the resulting ions using triple-quadrupole mass spectrometry in selected reaction monitoring mode. For 79 of the 90 metabolites, the assay is linear with a limit of detection of 10 ng/mL or less. Using this method, 36 metabolites can be reliably detected in extracts of the bacterium Salmonella enterica, with the identity of each metabolite confirmed by the presence, on growing of the bacteria in (13)C-glucose, of a peak corresponding to the isotope-labeled form of the compound. Quantitation in biological samples is performed by mixing unlabeled test cell extract with (13)C-labeled standard extract, and determining the (12)C/(13)C-ratio for each metabolite. Using this approach, the metabolomes of growing (exponential phase) and carbon-starved (stationary phase) bacteria were compared, revealing 16 metabolites that are significantly down-regulated and five metabolites that are significantly up-regulated, in stationary phase.     

Reduction of imines by hydroxycyclopentadienyl ruthenium hydride: intramolecular trapping evidence for hydride and proton transfer outside the coordination sphere of the metal

Reduction of imines by [2,5-Ph2-3,4-Tol2(eta(5)-C4COH)]Ru(CO)2H (2) produces kinetically stable ruthenium amine complexes. Reduction of an imine by 2 in the presence of an external amine trap gives only the complex of the newly generated amine. Reaction of 2 with H2N-p-C6H4N=CHPh (11), which contains an intramolecular amine trap, gave a 1:1 mixture of [2,5-Ph2-3,4-Tol2(eta(4)-C4CO)](CO)2RuNH(CH2Ph)(C6H4-p-NH2) (8), formed by coordination of the newly generated amine to the ruthenium center, and [2,5-Ph2-3,4-Tol2(eta(4)-C4CO)](CO)2RuNH2C6H4-p-NHCH2Ph (9), formed by coordination of the amine already present in the substrate. These results require transfer of hydrogen to the imine outside the coordination sphere of the metal to give a coordinatively unsaturated intermediate that can be trapped inside the initial solvent cage. Amine diffusion from the solvent cage must be much slower than coordination to the metal center. Mechanisms requiring prior coordination of the substrate to ruthenium would have led only to 8 and can be eliminated.     

Reactions involving transition metals : XIX. Some reactions of perfluoronorbornadiene with low valent transition metal complexes

Perfluoronorbornadiene reacts with the compounds [M(PPh₃)₄] (M = Pt, Pd) and [IrCl(CO)(PMePh₂)₂] to give the adducts [(C₇F₈)M(PPh₃)₂] and [(C₇F₈)IrCl(CO)(PMePh₂)₂] in which one of the double bonds is coordinated to the metal atom. The platinum complex reacts further with [Pt(PPh₃)₄] to give [(C₇F₈){Pt(PPh₃)₂}₂] having both double bonds coordinated to a Pt atom. The carbonylmetal anions [M^?] react to form the mono-substitution products [(C₇F₇)M] (M = Mn(CO)₅, Re(CO)₅, Ir(CO)₂(PPh₃)₂, Rh(CO)₂(PPh₃)₂), but the use of an excess of [Fe(CO)₂(η-C₅H₆)]^? leads to substitution of one fluorine atom on each of the double bonds. The complex having M = Mn(CO)₅ reacts with [Pt(PPh₃)₄] to afford the derivative [(C₇F₇){Mn(CO)₄(PPh₃)}{Pt(PPh₃)₂}], and the compound where M = Ir(CO)₂(PPh₃)₂ undergoes an oxidative addition reaction with acetyl chloride. Oxidative coupling products have been isolated on UV irradiation of a mixture of perfluoronorbornadiene and [Fe(η⁴-CH₂CRCHCH₂)(CO)₃] (R = H, Me), and under similar conditions the reaction with Fe(CO)₅ affords [(C₇F₈)Fe(CO)₄] in very low yield.     

Dynamic spin-polarized resonant tunneling in magnetic tunnel junctions

Precisely engineered tunnel junctions exhibit a long sought effect that occurs when the energy of the electron is comparable to the potential energy of the tunneling barrier. The resistance of metal-insulator-metal tunnel junctions oscillates with an applied voltage when electrons that tunnel directly into the barrier's conduction band interfere upon reflection at the classical turning points: the insulator-metal interface and the dynamic point where the incident electron energy equals the potential barrier inside the insulator. A model of tunneling between free electron bands using the exact solution of the Schr?dinger equation for a trapezoidal tunnel barrier qualitatively agrees with experiment.     

Determination of benzene in soft drinks and other beverages by isotope dilution headspace gas chromatography/mass spectrometry

An automated, simple, and reproducible method was developed for the determination of benzene in soft drinks, based on isotope dilution headspace gas chromatography/mass spectrometry in the selected-ion monitoring mode. The method was used to assess benzene levels in samples of 124 soft drinks and beverages. Benzene was not detected in 60% of the 124 products. The average benzene levels in 6 products exceeded the Canadian maximum acceptable concentration of 5 microg/L for benzene in drinking water, and 2 of the 6 products had benzene levels above the World Health Organization guideline of 10 microg/L. The highest level of benzene, 23 microg/L, was found in a soft drink product specifically marketed to children.     

Identification of potential small molecule peptidomimetics similar to motifs in proteins

Protein-protein interactions are central to most biological processes and represent a large and important class of targets for human therapeutics. Small molecules containing peptide substituents may mimic regions of interacting proteins and inhibit their interactions. We set out to develop efficient methods to screen for similarities between known peptide structures within proteins and small molecules. We developed a method to rank peptide-compound similarities, that is restricted to small linear motifs in proteins, and to compounds containing amino acid substituents. Application to a search of the PubChem database (5.4 million compounds) using all short motifs on accessible surface areas in a nonredundant set of 11 488 peptides from the protein structure database PDB demonstrated the feasibility of the method for high throughput comparisons and the availability of compounds with comparable substituents: over 6 million compound-peptide pairs shared at least three amino acid substituents, approximately 100 000 of which had an rmsd score of less than 1 A. A Z-score function was developed that compares matches of a compound to different instances of the peptide motif in PDB, providing an appropriate scoring function for comparison among peptide-compound similarities involving different numbers of atoms (while simultaneously enriching for similarities that are likely to be more specific for the protein of interest). We applied the method to searches of known short protein motifs against the National Cancer Institute Developmental Therapeutic Program compound database, identifying a known true positive.     

On the nature of the oxidative heterocoupling of lithium enolates

The coupling of enolates through single-electron oxidation is one of the most direct routes for generating 1,4-dicarbonyls. Recent work on the intermolecular heterocoupling of equimolar amounts of two different enolates through single-electron oxidation has shown that synthetically useful yields beyond those predicted by statistics can be obtained. To determine the underlying basis for the selective formation of heterocoupled products, kinetic, (7)Li NMR, and synthetic studies were performed. The collection of data obtained from these experiments shows that the selective formation of heterocoupled products is a consequence of heteroaggregation of lithium enolates.     

Determination of post-culture processing with carbohydrates by MALDI-MS and TMS derivatization GC-MS

Biological materials generally require stabilization to retain activity or viability in a dry form. A number of industrial products, such as vaccines, probiotics and biopesticides have been produced as dry preparations. The same methods and materials used for stabilizing commercial microbial products may be applicable to preserving biothreat pathogens in a dry form. This is a likely step that may be encountered when looking at samples from terrorism attempts since only spores, such as those from Bacillus anthracis, are inherently stable when dried. The stabilizers for microbial preparations generally include one or more small carbohydrates. Different formulations have been reported for different industrial products and are often determined empirically. However sugar alcohols (mannitol and sorbitol) and disaccharides (lactose, sucrose and trehalose) are the common constituents of these formulations. We have developed an analytical method for sample preparation and detection of these simple carbohydrates using two complementary analytical tools, MALDI-MS and GC-MS. The native carbohydrates and other constituents of the formulation are detected by MALDI-MS as a screening tool. A longer and more detailed analysis is then used to specifically identify the carbohydrates by derivatization and GC-MS detection. Both techniques were tested against ten different types of stabilization recipes with Yersinia pestis cell mass cultured on different media types used as the biological component. A number of additional components were included in these formulations including proteins and peptides from serum or milk, polymers (e.g. poly vinyl pyrrolidone - PVP) and detergents (e.g. Tween). The combined method was characterized to determine several figures of merit. The accuracy of the method was 98% for MALDI-MS and 100% for GC-MS. The repeatability for detection of carbohydrates by MALDI-MS was determined to be 96%. The repeatability of compound identification by GC-MS was determined by monitoring variation in retention time, which is vital for identification of isomeric carbohydrates. The figures of merit illustrate an effective and accurate method for mono and disaccharide detection independent of formulation. This meets our primary goal for method development as small carbohydrates are among the most common stabilizers employed.