Improvement of ZrC/Zr Coating on the Interface Combination and Physical Properties of Diamond-Copper Composites Fabricated by Spark Plasma Sintering.

In this study, diamond-copper composites were prepared with ZrC/Zr-coated diamond powders by spark plasma sintering. The magnetron sputtering technique was employed to coat the diamond particles with a zirconium layer. After heat treatment, most of the zirconium reacted with the surface of diamond and was transformed into zirconium carbide. The remaining zirconium on the zirconium carbide surface formed the outer layer. Owing to the method used to produce the ZrC/Zr-coated diamond in this study, the maximum thermal conductivity (TC) of 609 W·m-1·K-1 was obtained for 60 vol. % diamond-copper composites and the corresponding coefficient of thermal expansion (CTE) reached as low as 6.75 × 10-6 K-1. The bending strength of 40 vol. % ZrC/Zr-coated diamond-copper composites reached 255.95 MPa. The thermal and mechanical properties of ZrC/Zr-coated diamond-copper composites were substantially superior to those of uncoated diamond particles. Excellent properties can be attributed to the strengthening of the interfacial combination and the decrease in the interfacial thermal resistance due to the improvement associated with the ZrC/Zr coating. Theoretical analysis was also proposed to compare the thermal conductivities and CTE of diamond-copper composites fabricated with these two kinds of diamond powders.

Predicting post-translational lysine acetylation using support vector machines.

MOTIVATION: Lysine acetylation is a post-translational protein modification and a primary regulatory mechanism that controls many cell signaling processes. Lysine acetylation sites are recognized by acetyltransferases and deacetylases through sequence patterns (motifs). Recently, we used high-resolution mass spectrometry to identify 3600 lysine acetylation sites on 1750 human proteins covering most of the previously annotated sites and providing the most comprehensive acetylome so far. This dataset should provide an excellent source to train support vector machines (SVMs) allowing the high accuracy in silico prediction of acetylated lysine residues. RESULTS: We developed a SVM to predict acetylated residues. The precision of our acetylation site predictor is 78% at 78% recall on input data containing equal numbers of modified and non-modified residues. AVAILABILITY: The online predictor is available at http://www.phosida.com CONTACT: mmann@biochem.mpg.de

High-accuracy identification and bioinformatic analysis of in vivo protein phosphorylation sites in yeast.

Protein phosphorylation is a fundamental regulatory mechanism that affects many cell signaling processes. Using high-accuracy MS and stable isotope labeling in cell culture-labeling, we provide a global view of the Saccharomyces cerevisiae phosphoproteome, containing 3620 phosphorylation sites mapped to 1118 proteins, representatively covering the yeast kinome and a multitude of transcription factors. We show that a single false discovery rate for all peptide identifications significantly overestimates occurrence of rare modifications, such as tyrosine phosphorylation in yeast. The identified phosphorylation sites are predominantly located on irregularly structured and accessible protein regions. We found high evolutionary conservation of phosphorylated proteins and a large overlap of significantly over-represented motifs with the human phosphoproteome. Nevertheless, phosphorylation events at the site level were not highly conserved between yeast and higher eukaryotes, which points to metazoan-specific kinase and substrate families. We constructed a yeast-specific phosphorylation sites predictor on the basis of a support vector machine, which - together with the yeast phosphorylation data - is integrated into the PHOSIDA database (www.phosida.com).

Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis.

Complex protein mixtures have traditionally been separated by 2-DE. Görg introduced IPGs as the first dimension of protein separation. In recent years, MS-based proteomics has increasingly become the method of choice for identifying and quantifying large number of proteins. In that technology, to decrease analyte complexity, proteins are often separated by 1-D SDS-gel electrophoresis before online MS analysis. Here, we investigate a recently introduced device for peptide separation with IPGs (Agilent OFFGEL). Loading capacity for optimal peptide focusing is below 100 microg and--similar to 2-D gels--IEF is more efficient in the acidic than the basic pH region. The 24-well fractionation format resulted in about 40% additional peptide identifications but less than 20% additional protein identifications than the 12-well format. Compared to in-gel digestion, peptide IEF consistently identified a third more proteins with equal number of fractions. Low protein starting amounts (10 microg) still resulted in deep proteome coverage. Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics.

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites.

PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites.