Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.      

A close analysis of metal-enhanced fluorescence of tryptophan induced by silver nanoparticles: wavelength emission dependence

In the last few years, silver nanoparticles have been proposed as a promising alternative for the label-free detection of proteins via metal-enhanced fluorescence. Generally, the aromatic amino acid tryptophan is most frequently used in this type of studies, because the intrinsic fluorescence of proteins is usually dominated by tryptophan emissions. In the present study, we evaluated the fluorescence behavior of tryptophan in the presence of a silver colloid with nanoparticles of 100 nm in diameter. The results showed that a nanoparticles concentration of 32 mg L^?1 induced maximum fluorescence enhancement. However, the metal-enhanced fluorescence was dependent on the emission wavelength of tryptophan, and this phenomenon was closely related to the metal surface reabsorption process (inner filter effect), suggesting that the plasmon resonance reabsorption effect should be taken into account in analyses involving protein studies by metal-enhanced fluorescence.     

The zwitterionic structure of 2‐hydroxy‐4‐[(2‐hydroxybenzylidene)amino]benzoic acid

The title compound, C₁₄H₁₁NO₄, exists in the solid phase in the zwitterionic form, 2‐{[(4‐carboxy‐3‐hydroxyphenyl)iminiumyl]methyl}phenolate, with the H atom from the phenol group on the 2‐hydroxybenzylidene ring transferred to the imine N atom, resulting in a strong intramolecular N—H...O hydrogen bond between the iminium H atom and the phenolate O atom, forming a six‐membered hydrogen‐bonded ring. In addition, there is an intramolecular O—H...O hydrogen bond between the carboxylic acid group and the adjacent hydroxy group of the other ring, and an intermolecular C—H...O contact involving the phenol group and the C—H group adjacent to the imine bond, connecting the molecules into a two‐dimensional network in the (10) plane. π–π stacking interactions result in a three‐dimensional network. This study is important because it provides crystallographic evidence, supported by IR data, for the iminium zwitterionic form of Schiff bases.<!?tpb=12pt>     

Comparison of an antibody and its recombinant derivative for the detection of the small molecule explosive 2,4,6-trinitrotoluene

Antibodies are commonly used as recognition elements in immunoassays because of their high specificity and affinity, and have seen extensive use in competitive assays for the detection of small molecules. However, these complex molecules require production either in animals or by mammalian cell cultures, and are not easily tailored through genetic manipulation. Single chain antibodies (scFv), recombinantly expressed molecules consisting of only the antibody's binding region joined via a linking peptide, can provide an alternative to intact antibodies. We describe the characterization of a new monoclonal antibody (mAb), 2G5B5, able to detect the small molecule explosive 2,4,6-trinitrotoluene (TNT) and the scFv derived from its variable regions. The mAb and scFv were tested by surface plasmon resonance to determine their affinity for an immobilized TNT surrogate; dissociation constants were determined to be 1.5 × 10⁻¹³ M and 4.8 × 10⁻¹⁰ M respectively. Circular dichroism was used to determine their melting temperatures. The mAb is more stable melting at ∼75 °C while the scFv melts at ∼65 °C. The recognition elements were incorporated into a competitive assay format using a bead-based multiplexing platform to examine their sensitivity and specificity. The scFv was able to detect TNT ∼10-fold more sensitively than the mAb in this assay format, allowing detection of TNT concentrations down to at least 1 μg L⁻¹. The 2G5B gave similar detection limits to a commercial anti-TNT mAb, but was less specific, recognizing 1,3,5-trinitrobenzene (TNB) equally well as TNT.     

Synthesis of New Five Membered Nitrogen Containing Heterocycles Bearing D-Galactose Side Chains

The synthesis of 5-[6′-deoxy-(1′,2′:3′,4′-di-O-isopropylidene-α-D-galactopyranos-6′-yl)]tetrazole and its reaction with acetic anhydride and 1,2:3,4-di-O-isopropylidene-6-O-(4-toluenesulfonyl)-α-D-galactopyranose are described.     

Novel Synthesis of Some 1-N-(3-Fluoroadamantyl) Ureas

Some 1-N (3-fluoroadamantyl) ureas have been synthesized in good to excellent yields from 1-N- (3-fluoroadamantyl) isocyanate. The 3-fluoroadamantyl isocyanate has been prepared via the reaction of 1-N-(3-fluoroadamantyl) carboxamide with lead tetraacetate in N, N-dimethylformamide.     

Correlation of the Solubilizing Abilities of 1-Butyl-1-methyl-pyrrolidinium Tris(pentafluoroethyl)trifluorophosphate, 1-Butyl-1-methylpyrrolidinium Triflate and 1-Methoxyethyl-1-methylmorpholinium Tris(pentafluoroethyl)trifluorophosphate

Chromatographic retention data were measured for a wide range of organic solutes on 1-butyl-1-methylpyrolidinium tris(pentafluoroethyl)trifluorophosphate ([BMPyrr]⁺[FAP]^?), 1-butyl-1-methylpyrrolidinium triflate, ([BMPyrr]⁺[Trif]^?), and 1-methoxyethyl-1-methylmorpholinium tris(pentafluoroethyl)trifluorophosphate, ([MeoeMMorp]⁺[FAP]^?), stationary phases at (323, 353 and 383) K. The measured retention factors were combined with published infinite dilution activity coefficient and gas-to-water partition coefficient data to yield gas-to-anhydrous ionic liquid (IL) and water-to-anhydrous IL partition coefficients. The three sets of partition coefficients were analyzed using the Abraham model. The derived Abraham model correlations describe the observed gas-to-IL (log₁₀ K) and water-to-IL (log₁₀ P) partition coefficient data to within average standard deviations of about 0.11 and 0.15 log₁₀ units, respectively.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

Anticoincidence INAA capabilities for analysis of FDA Total Diet Study seafoods

Anticoincidence instrumental neutron activation analysis was used to analyze three portions each of five fresh-weight FDA Total Diet Study seafoods from 3 Market Basket collections for fiscal years 2006–2008. Portions were treated with l-cysteine solutions to enhance retention of Hg during irradiation then dried at room temperature over magnesium perchlorate. Results or limits of detection were obtained for 33 elements. In general, results agreed with those available from FDA’s Kansas city field laboratory (KAN-DO). Of three shrimp composites analyzed, one showed mass fractions of Ag, Fe, rare earths, U, Th, and Mo significantly higher (up to a factor of 10) than the other two shrimp composites. The same shrimp composite showed a lower Hg result (about 50 % after accounting for any irradiation loss) compared to the KAN-DO value. This may represent a drying loss. There were other indications of Hg loss during the drying process. SRM 1947 Lake Michigan Fish Tissue, run as a control, yielded an INAA Hg mass fraction 20 % lower (corrected for irradiation losses) than the certified value, similar to the difference between the INAA (0.171 mg/kg Hg) and KAN-DO (0.211 mg/kg Hg) results for a TDS canned tuna composite. Because previous studies showed that l-cysteine effectively sequesters inorganic Hg, these discrepancies likely represent methyl mercury loss. INAA results for As, Fe, Rb, and Se were in good agreement with SRM 1947 certified values.     

Comparisons of the vector method and tensor method for simulating liquid crystal devices

In calculating the director configuration in a liquid crystal device, two methods are commonly employed: a vector model and a tensor model. In this paper, we compare and contrast these methods for liquid crystal devices consisting of a layer of liquid crystal sandwiched between two plates. We compare the reliability and accuracy of the results, the speed of computation and the complexity of implementations of each method.