We report the studies on the mechanism of oxidation of 3',4'-dihydroxy-l-phenylalanine (l-DOPA) to neurotoxic dopachrome catalyzed by enzyme horseradish peroxidase (EC 1.11.1.7) using the kinetic (KIE), and solvent (SIE), isotope effect methods. For kinetic studies two specifically deuterated isotopomers: [2',5',6'-2H3]-l-DOPA was synthesized by the acid catalyzed isotopic exchange between nati...

Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil stru...

A mass spectrometry-based method is described for simultaneous identification and quantitation of individual proteins and for determining changes in the levels of modifications at specific sites on individual proteins. Accurate quantitation is achieved through the use of whole-cell stable isotope labeling. This approach was applied to the detection of abundance differences of proteins present i...

Proline-rich sequences (PRS) and their recognition domains have emerged as transposable protein interaction modules during eukaryotic evolution. They are especially abundant in proteins associated with pre-mRNA splicing and likely assist in the formation of the spliceosome by binding to GYF and WW domains. Here we profile PRS-mediated interactions of the CD2BP2/52K GYF domain by a site-specific...

Abstract. Water stable isotopes (?18O and ?2H) were analyzed in samples collected lakes, associated with riverine systems northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water at (a) lake shores (sampled March July 2020), (b) buoys which temporarily installed deep parts of the monthly to October (c) multiple spati...

The isotope record of the Danube River water at Vienna station probably is the longest dataset of a large river worldwide: 3H record since 1963, stable isotopes 2H and 18O records since 1968. From the 2H-18O relation (“deuterium excess”) can be concluded that the isotopic composition in the Danube River water reflects mainly the isotopic relations in the precipitation in the catchment area with...

An overview is provided of six strategies for relative or absolute quantitation of protein abundances that are widely used in proteomic studies. Strengths and limitations are discussed. Four of these involve stable isotope labeling and isotope ratio measurements by mass spectrometry. In another, mass spectra are used to deconvolute overlapping peptide HPLC peaks to provide relative quantitation...

Quantitative proteomics, based on stable isotope labeling by amino acids in cell culture (SILAC), can be used to identify host proteins involved in the intracellular interplay with pathogens. This method allows identification of proteins subject to degradation or upregulation in response to intracellular infection. It can also be used to study intracellular dynamics (trafficking) of proteins in...

An approach to proteomic analysis that combines bioorthogonal noncanonical amino acid tagging (BONCAT) and pulsed stable isotope labeling with amino acids in cell culture (pSILAC) provides accurate quantitative information about rates of cellular protein synthesis on time scales of minutes. The method is capable of quantifying 1400 proteins produced by HeLa cells during a 30 min interval, a tim...

Myelination depends on the synthesis of large amounts of myelin transcripts and proteins and is controlled by Nrg1/ErbB/Shp2 signaling. We developed a novel pulse labeling strategy based on stable isotope labeling with amino acids in cell culture (SILAC) to measure the dynamics of myelin protein production in mice. We found that protein synthesis is dampened in the maturing postnatal peripheral...