Porphyrin-containing molecular capsules: metal mediated dimerization of a bis-porphyrin cavity

[reaction] A self-complementary V-shaped bis-porphyrin cavity has been synthesized that is capable of dimerization to form a capsule structure. Self-assembly of the dimer occurs via metal ion coordination and produces an internal volume for guest encapsulation.     

Dysregulation of Na+/K+ ATPase by amyloid in APP+PS1 transgenic mice

Background  

The pathology of Alzheimer's disease (AD) is comprised of extracellular amyloid plaques, intracellular tau tangles, dystrophic neurites and neurodegeneration. The mechanisms by which these various pathological features arise are under intense investigation. Here, expanding upon pilot gene expression studies, we have further analyzed the relationship between Na+/K+ ATPase and amyloid using APP+PS1 transgenic mice, a model that develops amyloid plaques and memory deficits in the absence of tangle formation and neuronal or synaptic loss.     

Identification of proteases employed by dendritic cells in the processing of protein purified derivative (PPD)

Dendritic cells (DC) are known to present exogenous protein Ag effectively to T cells. In this study we sought to identify the proteases that DC employ during antigen processing. The murine epidermal-derived DC line Xs52, when pulsed with PPD, optimally activated the PPD-reactive Th1 clone LNC.2F1 as well as the Th2 clone LNC.4k1, and this activation was completely blocked by chloroquine pretreatment. These results validate the capacity of XS52 DC to digest PPD into immunogenic peptides inducing antigen specific T cell immune responses. XS52 DC, as well as splenic DC and DCs derived from bone marrow degraded standard substrates for cathepsins B, C, D/E, H, J, and L, tryptase, and chymases, indicating that DC express a variety of protease activities. Treatment of XS52 DC with pepstatin A, an inhibitor of aspartic acid proteases, completely abrogated their capacity to present native PPD, but not trypsin-digested PPD fragments to Th1 and Th2 cell clones. Pepstatin A also inhibited cathepsin D/E activity selectively among the XS52 DC-associated protease activities. On the other hand, inhibitors of serine proteases (dichloroisocoumarin, DCI) or of cystein proteases (E-64) did not impair XS52 DC presentation of PPD, nor did they inhibit cathepsin D/E activity. Finally, all tested DC populations (XS52 DC, splenic DC, and bone marrow-derived DC) constitutively expressed cathepsin D mRNA. These results suggest that DC primarily employ cathepsin D (and perhaps E) to digest PPD into antigenic peptides.     

Protein microarray scanning in label-free format by Kelvin nanoprobe

Surface-immobilized protein species deposited in the microarray format have been detected by time-of-flight secondary ion mass spectrometry and by scanning Kelvin nanoprobe. The former method was used to examine the nature of protein deposition on amine-coated glass slides and gold substrates in preparation for Kelvin measurements. Both gallium and SF(5)(+) ion sources were employed to produce positive and negative ion spectra of amino acids and polypeptides. Scanning Kelvin technology has been used to detect antibody-antigen interactions in a label-free protocol through measurement of the surface potential of the biochemical pair on indium tin oxide, amine-treated slides and gold substrates. The results show that good inter-spot reproducibility can be achieved and that deposited areas can be examined for homogeneity at 100 nm resolution. This work represents the first report on surface potential detection in protein microarray technology.     

Gas chromatography/mass spectrometry versus liquid chromatography/fluorescence detection in the analysis of phenols in mainstream cigarette smoke

A new gas chromatographic/mass spectrometric (GC/MS) technique for the analysis of hydroxybenzenes (phenols) in mainstream cigarette smoke has been developed. The technique allows the measurement of 24 individual compounds, and the sum of a few other alkyl-dihydroxybenzenes. A critical evaluation is done for the new technique and for an established high-performance liquid chromatographic (HPLC) technique reported in the literature for the analysis of hydroxybenzenes in cigarette smoke, which uses fluorescence detection. Compared with the HPLC procedure, the new technique has similar accuracy, precision, and robustness. However, the GC/MS procedure allows for a larger number of phenols to be analyzed simultaneously, and eliminates any potential interference that may appear in the HPLC method. Using the GC/MS analysis, it was found that besides the main phenols typically measured in mainstream cigarette smoke such as phenol, catechol, hydroquinone, and cresols, many other phenols that are present at lower levels can be quantitated in mainstream cigarette smoke.     

Characterization of the nanostructure of complexes formed by a redox-active cationic lipid and DNA

We report characterization of the nanostructures of complexes formed between the redox-active lipid bis(n-ferrocenylundecyl)dimethylammonium bromide (BFDMA) and DNA using small-angle neutron scattering (SANS) and cryogenic transmission electron microscopy (cryo-TEM). A particular focus was directed to the influence of lipid oxidation state (where reduced BFDMA has a net charge of +1 and oxidized BFDMA has a charge of +3) on the nanostructures of the solution aggregates formed. Complexes were characterized over a range of charge ratios of reduced BFDMA to DNA (1.1:1, 2.75:1, and 4:1) in solutions of 1 mM Li2SO4. For these complexes, a single peak in the SANS data at 1.2 nm(-1) indicated that a nanostructure with a periodicity of 5.2 nm was present, similar to that observed with complexes of the classical lipids DODAB/DOPE and DNA (multilamellar spacing of 7.0 nm). The absence of additional Bragg peaks in all the SANS data indicated that the periodicity did not extend over large distances. Both inverse Fourier transform analysis and form factor fitting suggested formation of a multilamellar vesicle. These results were confirmed by cryo-TEM images in which multilamellar complexes with diameters between 50 and 150 nm were observed with no more than seven lamellae per aggregate. In contrast to complexes of reduced BFDMA and DNA, Bragg peaks were absent in SANS spectra of complexes formed by oxidized BFDMA and DNA at all charge ratios investigated. The low-q behavior of the SANS data obtained using oxidized BFDMA and DNA complexes suggested that large, loose aggregates were formed, consistent with complementary cryo-TEM images showing predominantly loose disordered aggregates. Some highly ordered spongelike and cubic phase nanostructures were also detected in cryo-TEM images. We conclude that control of BFDMA oxidation state can be used to manipulate the nanostructures of lipid-DNA complexes formed using BFDMA.     

Enhanced Methylarginine Characterization by Post-Translational Modification-Specific Targeted Data Acquisition and Electron-Transfer Dissociation Mass Spectrometry

When localizing protein post-translational modifications (PTMs) using liquid-chromatography (LC)-tandem mass spectrometry (MS/MS), existing implementations are limited by inefficient selection of PTM-carrying peptides for MS/MS, particularly when PTM site occupancy is sub-stoichiometric. The present contribution describes a method by which peptides carrying specific PTMs of interest-in this study, methylarginines-may be selectively targeted for MS/MS: peptide features are extracted from high mass accuracy single-stage MS data, searched against theoretical PTM-carrying peptide masses, and matching features are subjected to targeted data acquisition LC-MS/MS. Using trypsin digested Saccharomyces cerevisiae Npl3, in which evidence is presented for 18 methylarginine sites-17 of which fall within a glycine-arginine-rich (GAR) domain spanning <120 amino acids-it is shown that this approach outperforms conventional data dependent acquisition (DDA): when applied to a complex protein mixture featuring in vivo methylated Npl3, 95% more (P=0.030) methylarginine-carrying peptides are selected for MS/MS than DDA, leading to an 86% increase (P=0.044) in the number of methylated peptides producing Mascot ion scores ≥20 following electron-transfer dissociation (ETD). Notably, significantly more low abundance arginine methylated peptides (maximum ion intensities <6×10(4) cps) are selected for MS/MS using this approach relative to DDA (50% more in a digest of purified in vitro methylated Npl3). It is also demonstrated that relative to collision-induced dissociation (CID), ETD facilitates a 586% increase (P=0.016) in average Mascot ion scores of methylarginine-carrying peptides. The present PTM-specific targeted data acquisition approach, though described using methylarginine, is applicable to any ionizable PTM of known mass.     

Optimized thermal desorption for improved sensitivity in trace explosives detection by ion mobility spectrometry

In this work we evaluate the influence of thermal desorber temperature on the analytical response of a swipe-based thermal desorption ion mobility spectrometer (IMS) for detection of trace explosives. IMS response for several common high explosives ranging from 0.1 ng to 100 ng was measured over a thermal desorber temperature range from 60 °C to 280 °C. Most of the explosives examined demonstrated a well-defined maximum IMS signal response at a temperature slightly below the melting point. Optimal temperatures, giving the highest IMS peak intensity, were 80 °C for trinitrotoluene (TNT), 100 °C for pentaerythritol tetranitrate (PETN), 160 °C for cyclotrimethylenetrinitramine (RDX) and 200 °C for cyclotetramethylenetetranitramine (HMX). By modifying the desorber temperature, we were able to increase cumulative IMS signal by a factor of 5 for TNT and HMX, and by a factor of 10 for RDX and PETN. Similar signal enhancements were observed for the same compounds formulated as plastic-bonded explosives (Composition 4 (C-4), Detasheet, and Semtex). In addition, mixtures of the explosives exhibited similar enhancements in analyte peak intensities. The increases in sensitivity were obtained at the expense of increased analysis times of up to 20 seconds. A slow sample heating rate as well as slower vapor-phase analyte introduction rate caused by low-temperature desorption enhanced the analytical sensitivity of individual explosives, plastic-bonded explosives, and explosives mixtures by IMS. Several possible mechanisms that can affect IMS signal response were investigated such as thermal degradation of the analytes, ionization efficiency, competitive ionization from background, and aerosol emission.     

Facile Synthesis and Structural Characterization by NMR,ESI–MS/MS and DFT Calculations of New (E)‐6‐[2‐Ferrocenylalkylidenehydrazino]nicotinic Hydrazides and Their (E)‐Ferrocenyl‐pyrazolyl‐pyridine Heterocyclic System

This paper reports a facile and convenient access by a conventional thermal procedure in ethanol as solvent to a new examples of (E)‐6‐[2‐ferrocenylalkylidenehydrazino]nicotinic hydrazides ( 3 ) (53–72%) from the quimioselective reactions of 6‐hydrazinonicotinc hydrazide ( 1 ) with acylferrocenes ( 2 ), where acyl = formyl and acetyl. Subsequently, cyclocondensation reactions of ferrocenylalkylidene hydrazones ( 3 ) with 4‐R¹‐4‐alkoxy‐1,1,1‐trifluoroalk‐3‐en‐2‐ones ( 4 ), where R¹ = Me, Ph, 2‐Furyl, to obtain new six heterocyclic derivatives as (E)‐pyrazolyl‐pyridinohydrazones ( 5 ) (58–63%), are also presented. The structures of these new heterocyclic compounds 5 containing an organometallic unit were characterized and studied by NMR, ESI–MS/MS techniques. DFT calculations were also employed to assign the E configuration for compounds 3 and 5 .     

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.