Phosphorylation site localization in peptides by MALDI MS/MS and the Mascot Delta Score

Owing to its broad biological significance, the large-scale analysis of protein phosphorylation is more and more getting into the focus of proteomic research. Thousands of phosphopeptides can nowadays be identified using state-of-the-art tandem mass spectrometers in conjunction with sequence database searching, but localizing the phosphate group to a particular amino acid in the peptide sequence is often still difficult. Using 180 individually synthesized phosphopeptides with precisely known phosphorylation sites (p-sites), we have assessed the merits of the Mascot Delta Score (MD score) for the assignment of phosphorylation sites from tandem mass spectra (MS/MS) generated on four different matrix-assisted laser desorption ionization (MALDI) mass spectrometers including tandem time-of-flight (TOF/TOF), quadrupole time-of-flight, and ion trap mass analyzers. The results show that phosphorylation site identification is generally possible with false localization rates of about 10%. However, a comparison to previous work also revealed that phosphorylation site determination by MALDI MS/MS is less accurate than by ESI-MS/MS particularly if several and/or adjacent possible phosphorylation acceptor sites exist in a peptide sequence. We are making the tandem MS spectra and phosphopeptide collection available to the community so that scientists may adapt the MD scores reported here to their analytical environment and so that informatics developers may integrate the MD score into proteomic data analysis pipelines.     

Room temperature all‐silicon photonic crystal nanocavity light emitting diode at sub‐bandgap wavelengths

Silicon is now firmly established as a high performance photonic material. Its only weakness is the lack of a native electrically driven light emitter that operates CW at room temperature, exhibits a narrow linewidth in the technologically important 1300–1600 nm wavelength window, is small and operates with low power consumption. Here, an electrically pumped all‐silicon nano light source around 1300–1600 nm range is demonstrated at room temperature. Using hydrogen plasma treatment, nano‐scale optically active defects are introduced into silicon, which then feed the photonic crystal nanocavity to enhance the electrically driven emission in a device via Purcell effect. A narrow ( nm) emission line at 1515 nm wavelength with a power density of is observed, which represents the highest spectral power density ever reported from any silicon emitter. A number of possible improvements are also discussed, that make this scheme a very promising light source for optical interconnects and other important silicon photonics applications.     

Time scales of slow motions in ubiquitin explored by heteronuclear double resonance

Understanding how proteins function at the atomic level relies in part on a detailed characterization of their dynamics. Ubiquitin, a small single-domain protein, displays rich dynamic properties over a wide range of time scales. In particular, several regions of ubiquitin show the signature of chemical exchange, including the hydrophobic patch and the β4-α2 loop, which are both involved in many interactions. Here, we use multiple-quantum relaxation techniques to identify the extent of chemical exchange in ubiquitin. We employ our recently developed heteronuclear double resonance method to determine the time scales of motions that give rise to chemical exchange. Dispersion profiles are obtained for the backbone NH(N) pairs of several residues in the hydrophobic patch and the β4-α2 loop, as well as the C-terminus of helix α1. We show that a single time scale (ca. 50 μs) can be used to fit the data for most residues. Potential mechanisms for the propagation of motions and the possible extent of correlation of these motions are discussed.     

Chiral sulfamide-catalyzed asymmetric Michael addition of protected 3-hydroxypropanal to β-nitrostyrenes

Organocatalytic asymmetric Michael addition of 3-(OTBS)-propanal to β-nitrostyrenes catalyzed by chiral sulfamides was investigated. Good d.r. (up to 80:20) and excellent enantioselectivities (up to >99% ee) were achieved. Both the N-[(1R,2R)-2-aminocyclohexyl]-N’-(phenylmethyl)sulfamide 7b and the novel chiral N-[(1R,2R)-2-aminocyclohexyl]-N’-[3,5-bis(trifluoromethyl)phenyl]sulfamide 7a were identified as efficient primary amine organocatalysts.     

Determination of elements in blood of White New Zealand rabbits by NAA

The determination of elemental concentrations for Br, Ca, Cl, Fe, K, Mg, Na, S, Sr, and Zn in blood samples from White New Zealand rabbits was performed applying the NAA technique. Twenty whole blood samples (12 male and 8 female) collected in research centers from Brazil (Aggeu Magalhães in Recife and Butantan Institute in São Paulo) were investigated, using the IEA-R1 nuclear reactor at IPEN/CNEN-SP-Brazil. These data can be used as references to perform biochemistry analyses in veterinary medicine using small quantities of whole blood (100–400 μL), simplifying the collection and the preparation of biological samples (it is not necessary to perform the serum separation nor to use specific reactants). Furthermore, the knowledge of the biochemical values in blood allows us to check the similarities with the blood estimations in human beings, which is an important condition for selecting laboratory animals. Finally, these data suggest a great similarity of the inorganic tissue profile of rabbits (White New Zealand) and humans.     

Analysis of saliva from <Emphasis Type="Italic">Amblyomma cajennense</Emphasis> (Acari: Ixodidae) species from Brazil by NAA

The Amblyomma cajennense tick species is considered one of the most important and widespread species in Brazil. It salivary secretion has been a target of several studies in biocenology, as the vector of diseases and in investigations related to antihemostatic properties and antitumor. To complement this investigation, neutron activation analysis (NAA) was applied to determine concentrations of elements in saliva samples of this tick species. The saliva samples (50–554 μL) were collected at Butantan Institute (São Paulo city, Brazil) and they were investigated using the IEA-R1 nuclear reactor at IPEN/CNEN-SP-Brazil. These data were compared with the values established for Amblyomma americanum and Amblyomma variegatum species emphasizing agreement only for Cl, K and Na with the A. americanum species, suggesting similarities in the mechanisms that regulate the osmotic pressure in this hematophagous animal. The knowledge of these limits contributes for tick saliva characterization as well as for the understanding of the many physiological processes, especially those related to salivary secretion.     

Further Withaphysalin Derivatives from Acnistus arborescens

Two new epimeric chlorinated withaphysalins, rel‐(4β,5β,6α,18S,22R)‐ and rel‐(4β,5β,6α,18R,22R)‐6‐chloro‐18,20‐epoxy‐18‐ethoxy‐4,5‐dihydroxy‐1‐oxowitha‐2,24‐diene‐26,22‐lactone ( 1 and 2 resp.), together with the new rel‐(4β,5β,6α,18R,22R)‐6‐chloro‐18,20‐epoxy‐4,5‐dihydroxy‐18‐methoxy‐1‐oxowitha‐2,24‐diene‐26,22‐lactone ( 3 ) and rel‐(3β,4β,5β,6β,18R,22R)‐5,6:18,20‐diepoxy‐3,18‐diethoxy‐4‐hydroxy‐1‐oxowith‐24‐ene‐26,22‐lactone ( 4 ) were isolated from the leaves of Acnistus arborescens and named withaphysalins T–W, respectively. The final structures and the complete ¹H‐ and ¹³C‐NMR assignments of the three chlorowithaphysalins 1 – 3 were performed by means of HR‐ESI‐MS and 1D‐ and 2D‐NMR experiments, including COSY, HSQC, and HMBC, beside comparison with spectral data of analogous compounds from the literature. The structure of 4 was also confirmed by means of a single‐crystal X‐ray diffraction analysis.     

Efficient Cluster-Based Catalysts for Asymmetric Hydrogenation of α-Unsaturated Carboxylic Acids

The new clusters [H(4) Ru(4) (CO)(10) (μ-1,2-P-P)], [H(4) Ru(4) (CO)(10) (1,1-P-P)] and [H(4) Ru(4) (CO)(11) (P-P)] (P-P=chiral diphosphine of the ferrocene-based Josiphos or Walphos ligand families) have been synthesised and characterised. The crystal and molecular structures of eleven clusters reveal that the coordination modes of the diphosphine in the [H(4) Ru(4) (CO)(10) (μ-1,2-P-P)] clusters are different for the Josiphos and the Walphos ligands. The Josiphos ligands bridge a metal-metal bond of the ruthenium tetrahedron in the "conventional" manner, that is, with both phosphine moieties coordinated in equatorial positions relative to a triangular face of the tetrahedron, whereas the phosphine moieties of the Walphos ligands coordinate in one axial and one equatorial position. The differences in the ligand size and the coordination mode between the two types of ligands appear to be reflected in a relative propensity for isomerisation; in solution, the [H(4) Ru(4) (CO)(10) (1,1-Walphos)] clusters isomerise to the corresponding [H(4) Ru(4) (CO)(10) (μ-1,2-Walphos)] clusters, whereas the Josiphos-containing clusters show no tendency to isomerisation in solution. The clusters have been tested as catalysts for asymmetric hydrogenation of four prochiral α-unsaturated carboxylic acids and the prochiral methyl ester (E)-methyl 2-methylbut-2-enoate. High conversion rates (>94?%) and selectivities of product formation were observed for almost all catalysts/catalyst precursors. The observed enantioselectivities were low or nonexistent for the Josiphos-containing clusters and catalyst (cluster) recovery was low, suggesting that cluster fragmentation takes place. On the other hand, excellent conversion rates (99-100?%), product selectivities (99-100?% in most cases) and good enantioselectivities, reaching 90?% enantiomeric excess (ee) in certain cases, were observed for the Walphos-containing clusters, and the clusters could be recovered in good yield after completed catalysis. Results from high-pressure NMR and IR studies, catalyst poisoning tests and comparison of catalytic properties of two [H(4) Ru(4) (CO)(10) (μ-1,2-P-P)] clusters (P-P=Walphos ligands) with the analogous mononuclear catalysts [Ru(P-P)(carboxylato)(2) ] suggest that these clusters may be the active catalytic species, or direct precursors of an active catalytic cluster species.