Solid-supported synthesis of a peptide beta-turn mimetic

[structure: see text]The solid-supported synthesis of a bicyclic diketopiperazine, a potential peptide beta-turn mimetic, is described. The Ugi reaction between the resin ester of alpha-N-Boc-diaminopropionic acid (an amine input), alpha-bromo acid, aldehyde, and isocyanide is the key step in the proposed protocol.     

The application of C-N.M.R. spectroscopy to the determination of the stereochemistry of Diels-Alder adducts

Long-range (³J) ¹³C-H coupling is a reliable probe to evaluate the stereochemistry of cycloaddition products. The method is best applied to carbonyl containing adducts but not restricted to them. Several structures have been revised and new ones evaluated.     

Ion mobility–mass spectrometry: a new paradigm for proteomics

Matrix-assisted laser desorption/ionization (MALDI) coupled with ion mobility–mass spectrometry (IM–MS) provides a rapid (μs–ms) means for the two-dimensional (2D) separation of complex biological samples (e.g., peptides, oligonucleotides, glycoconjugates, lipids, etc.), elucidation of solvent-free secondary structural elements (e.g., helices, β-hairpins, random coils, etc.), rapid identification of post-translational modifications (e.g., phosphorylation, glycosylation, etc.) or ligation of small molecules, and simultaneous and comprehensive sequencing information of biopolymers. In IM–MS, protein-identification information is complemented by structural characterization data, which is difficult to obtain using conventional proteomic techniques. New avenues for enhancing the figures of merit (e.g., sensitivity, limits of detection, dynamic range, and analyte selectivity) and optimizing IM–MS experimental parameters are described in the context of deriving new information at the forefront of proteomics research.     

Gas chromatographic-mass spectrometric method for trazodone and a deuterated analogue in plasma

A plasma assay method for trazodone and a 2H4 analogue is described which uses gas chromatography--electron-impact selected-ion monitoring mass spectrometry. Etoperidone is used as an internal standard. The analytes are extracted from basic medium into n-butyl chloride, then back extracted into aqueous 0.1 M hydrochloric acid. The aqueous layer is made basic and re-extracted with n-butyl chloride. The solvent is reduced under nitrogen at 35 degrees C and the residue is redissolved in toluene for gas chromatographic--mass spectrometric analysis. The ions monitored are m/z 231, 235, and 225 for trazodone, [2H4] trazodone and etoperidone, respectively. Quantitation is in the range 40-1000 ng/ml with acceptable precision and accuracy. The method is suitable for biopharmaceutical studies.     

Direct transformation of ice VII′ to low-density amorphous ice

Vibrational spectra reveal that ice VII′ transforms to low-density amorphous ice (LDA) at low temperature on release of pressure to ambient pressure and low temperature. The measurements were obtained using in situ Raman spectroscopy of samples of ice VII′ as a function of pressure at 135 K. The observation of this direct decompression-induced VII′-LDA transition complements the previously observed pressure-induced reversible transition between LDA and high-density amorphous ice (HDA) at 120–140 K and the temperature-induced amorphization of metastable ice VII and ice VIII at 0.1 MPa.     

The role of acidic residues and of sodium ion adduction on the gas-phase H/D exchange of peptides and peptide dimers

Gas-phase H/D exchange is widely used for characterizing the structure of ions. However, many structural parameters that affect the rate of H/D exchange are poorly understood, which complicates the interpretation of experimental data. Here, the effects of sodium ion adduction on the rate of H/D exchange with D₂O for a series of peptides and peptide dimers with varying numbers of acidic residues are described. The maximum number of sodium ion adducts that can be accommodated by the peptides and peptide dimers in this study is N + 1, where N is the number of free carboxylic acid groups. The formation of methyl-esters at all carboxylic acid groups, or the replacement of all the acidic hydrogens with sodium ions, effectively shuts down H/D exchange with D₂O. In contrast, both the rate and the extent of H/D exchange with D₂O are increased for most of the peptides and peptide dimers by the adduction of an intermediate number of sodium ions. These results are consistent with the H/D exchange occurring via a salt-bridge mechanism and show that the presence of two carboxylic acid groups is much better than one. The results with peptide dimers also indicate that surface accessibility may not be a dominant factor in the extent of H/D exchange for these ions.     

An abundance of nodulation factors

In this issue of Chemistry & Biology, Morón et al. [1] report that Rhizobium tropici CIAT899 produces different Nod factors in response to flavonoid induction under differing environmental conditions. This unanticipated environmental dependence has implications for altering or potentially improving the host-bacteria interaction in bean nodulation.     

Size-selected (2-10 nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides

In this report, first use of size-selected gold nanoparticles (AuNPs) as matrixes for matrix assisted laser desorption/ionization (MALDI) is described for peptides and proteins. In comparison with conventional organic acid MALDI matrixes, the optimum matrix-to-analyte ratio with AuNP matrixes is reduced by 10-14 orders of magnitude. Significant differences in the relative abundances of the ions observed in positive and negative mode MALDI-time-of-flight mass spectrometry (TOFMS) are revealed as the AuNP size distribution is decreased from 10 to 2 nm, whereby 2-nm AuNPs exhibit quantum confinement effects prevalent in quantum dots. AuNP matrixes allow for selective analyte ionization, as demonstrated in the selective MALDI-TOFMS of phosphotyrosine in a background of phosphoserine and phosphothreonine peptides.     

Preparation and properties of surface modified ceramic membranes. Part III. Gas permeation of 5 nm alumina membranes modified by trichloro-octadecylsilane

Stable trichloro-octadecyl silane (ODS) derivatives of a 5 nm γ-alumina ceramic membrane were prepared. Gas permeabilities of the untreated membrane did not show Knudsen diffusion at 20°C. Gas permeabilities of the ODS membrane were three orders of magnitude lower; He, Ne, Ar, CO₂, C₃H₈ have near constant permeabilities 360 mol s⁻¹ m⁻² bar⁻¹, except methane which has the highest permeability of the group, 481 mol s⁻¹ m⁻² bar⁻¹. The mechanism of diffusion is solution/diffusion. Remarkably, permeabilities of ODS-alumina membrane were reduced by 5 X after exposure to a pressure difference of 1 atm (active layer side) against vacuum for only 10 min. The effect was metastable but could be reversed on standing for several hours, reversal of pressure difference or after washing with (hydrocarbon solvent) toluene. The mechanism was presumed to be due to movement of the octadecyl-hydrocarbon chains of the silane monolayer causing a partially blocked pore structure; perhaps a unique example of self-fouling.