Mass spectrometric characterization of lipid-modified peptides for the analysis of acylated proteins

The analysis of acylated proteins by mass spectrometry (MS) has largely been overshadowed in proteomics by the analysis of glycosylated and phosphorylated proteins; however, lipid modifications on proteins are proving to be of increasing importance in biomedical research. In order to identify the marker ions and/or neutral loss fragments that are produced upon collision-induced dissociation, providing a means to identify the common lipid modifications on proteins, peptides containing an N-terminally myristoylated glycine, a palmitoylated cysteine and a farnesylated cysteine were chemically synthesized. Matrix-assisted laser desorption/ionization time-of-flight time-of-flight (MALDI-TOF-TOF), electrospray ionization quadrupole time-of-flight (ESI Q-TOF), and electrospray ionization hybrid triple-quadrupole/linear ion trap (ESI QqQ(LIT)) mass spectrometers were used for the analysis. The peptide containing the N-terminally myristoylated glycine, upon CID, produced the characteristic fragments a1 (240.4 Th) and b1 (268.4 Th) ions as well as a low-intensity neutral loss of 210 Da (C14H26O). The peptides containing a farnesylated cysteine residue fragmented to produce a marker ion at a m/z of 205 Th (C15H25) as well as other intense farnesyl fragment ions, and a neutral loss of 204 Da (C15H24). The peptides containing a palmitoylated cysteine moiety generated neutral losses of 238 Da (C16H30O) and 272 Da (C16H32OS); however, no marker ions were produced. The neutral losses were more prominent in the MALDI-TOF-TOF spectra, whereas the marker ions were more abundant in the ESI QqQ(LIT) and Q-TOF mass spectra.     

Measurement of long-range 1H-19F scalar coupling constants and their glycosidic torsion dependence in 5-fluoropyrimidine-substituted RNA

Long-range scalar 5J(H1',F) couplings were observed in 5-fluoropyrimidine-substituted RNA. We developed a novel S3E-19F-alpha,beta-edited NOESY experiment for quantitation of these long-range scalar 5J(H1',F) couplings, where the J-couplings can be extracted from inspection of intraresidual (H1',H6) NOE cross-peaks. Quantum chemical calculations were exploited to investigate the relation between scalar couplings and conformations around the glycosidic bond in oligonucleotides. The theoretical dependence of the observed 5J(H1',F) couplings on the torsion angle chi can be described by a generalized Karplus relationship. The corresponding density functional theory (DFT) analysis is outlined. Additional NMR experiments facilitating the resonance assignments of 5-fluoropyrimidine-substituted RNAs are described, and chemical shift changes due to altered shielding in the presence of fluorine-19 (19F) are presented.     

Quiet imaging with interleaved spiral read-out

The acoustic noise generated during an MRI sequence can be effectively reduced with the help of soft gradient pulses using sinusoidal ramps. The long slope duration, however, leads to long acquisition times. The use of interleaved spiral trajectories, calculated with long gradient slopes, is proposed to reduce the acquisition time while maintaining low acoustic noise levels. The practibility of this approach is demonstrated on phantom and volunteer images.     

Rubidium-decaamidodichromat(III), Rb4Cr2(NH2)10 – Synthese und Kristallstruktur

Rubidium Decaamidodichromate(III), Rb₄Cr₂(NH₂)₁₀ – Synthesis and Crystal Structure The reaction of chromium(III) with rubidium amide in a molar ratio of Cr(NH₂)₃/RbNH₂ = 1 : 1.75 at 140 °C and p(NH₃) = 3 kbar in a high-pressure autoclave results after 90 days in dark violet crystals of Rb₄Cr₂(NH₂)₁₀. Structure determination was done by single crystal X-ray methods:Pna2₁ (No. 33), Z = 4, a = 12.244(3) Å, b = 6.727(1) Å, c = 19.775(5) Å, N(F²_o > 3σ(F²_o)) = 1046, N(Var.) = 94, R/R_w = 0,051/0,059&#TAB;The structure of Rb₄Cr₂(NH₂)₁₀ contains isolated, face-sharing N-octahedra around two Cr³⁺-ions giving [Cr(NH₂)₃(NH₂)_3/2]₂^3–. These are arranged to oneanother following the motif of a hexagonal closest packing. They are connected via Rb⁺- and one further amide ion not bound to Cr³⁺. The compound is characterized by thermoanalytical and IR-/Raman-spectroscopic measurements.     

Exploration of the variability of variable selection based on distances between bootstrap sample results

It is well known that variable selection in multiple regression can be unstable and that the model uncertainty can be considerable. The model uncertainty can be quantified and explored by bootstrap resampling, see Sauerbrei et al. (Biom J 57:531–555, 2015). Here approaches are introduced that use the results of bootstrap replications of the variable selection process to obtain more detailed information about the data. Analyses will be based on dissimilarities between the results of the analyses of different bootstrap samples. Dissimilarities are computed between the vector of predictions, and between the sets of selected variables. The dissimilarities are used to map the models by multidimensional scaling, to cluster them, and to construct heatplots. Clusters can point to different interpretations of the data that could arise from different selections of variables supported by different bootstrap samples. A new measure of variable selection instability is also defined. The methodology can be applied to various regression models, estimators, and variable selection methods. It will be illustrated by three real data examples, using linear regression and a Cox proportional hazards model, and model selection by AIC and BIC.

     

On structural stability for semiflows

Some results on structural stability which are known to hold for flows of a compact manifold are extended to semiflows of a Banach space.