Application of MeCAT-Click labeling for protein abundance characterization of E. coli after heat shock experiments.

In a proof of concept study, metal-coded affinity tags based on click chemistry (MeCAT-Click) were used to analyze the proteome of Escherichia coli (E. coli) in response to heat stress. This allows high labeling efficiency, high detection sensitivity, and multiplex capabilities, which are pivotal for its application to protein quantification. Two approaches are presented for relative quantification of differentially lanthanide-labeled proteins. The first approach uses isotope-labeling, where ESI-MS was utilized to quantify the differentially labeled proteins from different states of E. coli. With this approach, 14 proteins were found with changed abundance, among them five proteins upregulated. In the second approach, differentially labeled samples were separated by two dimensional gel electrophoresis (2-DE) and scanned by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Comparison of the signal intensities of the different lanthanides was used to quantify different sample states. Based on this information, ESI-MS was used to identify the proteins with different abundance. The sensitivity of LA-ICP-MS allowed us to find one upregulated protein that was nearly invisible by silver staining ("Probable replication endonuclease from retron EC67"). The advantage of this approach is to locate low abundant proteins with differential expression using LA-ICP-MS, which may be overlooked otherwise. BIOLOGICAL SIGNIFICANCE: This paper demonstrates the successful application of a novel metal labeling strategy to quantify the proteins from complex biological samples. In comparison with former metal labeling strategies, it reduces the steric hindrance and improves the labeling efficiency during the labeling process, which ensure its successful application. This methodology is compatible with both molecular and elemental mass spectrometry. ESI-MS/MS in combination with software-based search allows the identification and relative quantification of labeled proteins. In addition, LA-ICP-MS helps to locate the labeled proteins in 2-DE gels with superior detection capability, thus, target proteins with low abundance can be precisely followed. Its excellent sensitivity allows one to track the proteins of interest that are barely visible by silver staining.

Synthesis of active carbon-based catalysts by chemical vapor infiltration for nitrogen oxide conversion.

Direct reduction of nitrogen oxides is still a challenge. Strong efforts have been made in developing noble and transition metal catalysts on microporous support materials such as active carbons or zeolites. However, the required activation energy and low conversion rates still limit its breakthrough. Furthermore, infiltration of such microporous matrix materials is commonly performed by wet chemistry routes. Deep infiltration and homogeneous precursor distribution are often challenging due to precursor viscosity or electrostatic shielding and may be inhibited by pore clogging. Gas phase infiltration, as an alternative, can resolve viscosity issues and may contribute to homogeneous infiltration of precursors. In the present work new catalysts based on active carbon substrates were synthesized via chemical vapor infiltration. Iron oxide nano clusters were deposited in the microporous matrix material. Detailed investigation of produced catalysts included nitrogen oxide adsorption, X-ray diffraction, scanning electron microscopy and energy-dispersive X-ray spectroscopy. Catalytic activity was studied in a recycle flow reactor by time-resolved mass spectrometry at a temperature of 423 K. The infiltrated active carbons showed very homogeneous deposition of iron oxide nano clusters in the range of below 12 to 19 nm, depending on the amount of infiltrated precursor. The specific surface area was not excessively reduced, nor was the pore size distribution changed compared to the original substrate. Catalytic nitrogen oxides conversion was detected at temperatures as low as 423 K.

Shared solvation of sodium ions in alcohol-water solutions explains the non-ideality of free energy of solvation.

In order to explain the discrepancies between theories and experiments regarding the non-ideality in the free energy of solvation, here we present a microscopic picture of sodium ions dissolved in water-alcohol mixed solvents. We used X-ray absorption spectroscopy to probe the K-edge of sodium ions in mixed solvents of water and alcohols (methanol, ethanol) and in the respective pure solvents. In the mixed solvents a shared solvation of the sodium ions is observed. We find that specifically the water component plays a key role in stabilizing the solvation shell in mixed solvents, which was revealed by a selective photochemical process occurring only in the pure alcohol solvents.

The second extracellular loop of pore-forming subunits of ATP-binding cassette transporters for basic amino acids plays a crucial role in interaction with the cognate solute binding protein(s).

In the thermophile Geobacillus stearothermophilus, the uptake of basic amino acids is mediated by an ABC transporter composed of the substrate binding protein (receptor) ArtJ and a homodimer each of the pore-forming subunit, ArtM, and the nucleotide-binding subunit, ArtP. We recently identified two putative binding sites in ArtJ that might interact with the Art(MP)(2) complex, thereby initiating the transport cycle (A. Vahedi-Faridi et al., J. Mol. Biol. 375:448-459, 2008). Here we investigated the contribution of charged amino acid residues in the second extracellular loop of ArtM to contact with ArtJ. Our results demonstrate a crucial role for residues K177, R185, and E188, since mutations to oppositely charged amino acids or glutamine led to a complete loss of ArtJ-stimulated ATPase activity of the complex variants in proteoliposomes. The defects could not be suppressed by ArtJ variants carrying mutations in site I (K39E and K152E) or II (E163K and D170K), suggesting a more complex interplay than that by a single salt bridge. These findings were supported by cross-linking assays demonstrating physical proximity between ArtJ(N166C) and ArtM(E182C). The importance of positively charged residues for receptor-transporter interaction was underscored by mutational analysis of the closely related transporter HisJ/LAO-HisQMP(2) of Salmonella enterica serovar Typhimurium. While transporter variants with mutated positively charged residues in HisQ displayed residual ATPase activities, corresponding mutants of HisM could no longer be stimulated by HisJ/LAO. Interestingly, the ATPase activity of the HisQM(K187E)P(2) variant was inhibited by l- and d-histidine in detergent, suggesting a role of the residue in preventing free histidine from gaining access to the substrate binding site within HisQM.

Comprehensive profiling of the complex dendrimeric contrast agent Gadomer using a combined approach of CE, MS, and CE-MS.

The complex dendrimeric contrast agent Gadomer has been comprehensively characterized using various mass spectrometric techniques in combination with capillary electrophoresis. The analytical challenges arising from the structure of this analyte, e.g., the presence of a complex isotopic pattern originating from multiple gadolinium chelates could be overcome using this combined approach. Results obtained from initial MALDI-TOF-MS measurements could subsequently be complemented and confirmed by CE-ESI-TOF-MS measurements. Furthermore, high resolution Fourier transform-ion cyclotron resonance-MS (FT-ICR-MS) as a stand alone technique and in combination with CE was performed to obtain mass spectra of high mass accuracy and resolution of various impurities and related dendrimers present in low concentrations in several Gadomer batches. The profile of related dendrimers and impurities of lower molecular weight present in Gadomer could be elucidated and variances in the pattern of related dendrimers present in batches obtained via different synthetic routes could be detected. The qualitative analysis of Gadomer using MS techniques in combination with CE provides the fundamental basis for a framework of analytical methodologies for the characterization of Gadomer. By designing such a framework of methodologies the challenges associated with the introduction of dendrimers into the clinical stage may be overcome and the reproducible quality and safety of these innovative products can be ensured.