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Acetylation of histone H3 on lysine 56 occurs during mitotic and meiotic S phase in fungal species. This acetylation blocks a direct electrostatic interaction between histone H3 and nucleosomal DNA, and the absence of this modification is associated with extreme sensitivity to genotoxic agents. We show here that H3-K56 acetylation is catalyzed when Rtt109,(More)
MassMatrix is a program that matches tandem mass spectra with theoretical peptide sequences derived from a protein database. The program uses a mass accuracy sensitive probabilistic score model to rank peptide matches. The MS/MS search software was evaluated by use of a high mass accuracy dataset and its results compared with those from MASCOT, SEQUEST,(More)
The extent and pattern of histone post-translational modifications is a key determinant dictating the structure of chromatin. We employed mass spectrometry to map the post-translational modifications present on mammalian core histones. Using accurate peptide mass fingerprinting on proteolytic digests of purified histones, we identified more than 20 novel(More)
Full structural characterization of complex mixtures such as humic acid extracts has been elusive because of insufficient compound resolution with conventional techniques. Using electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry, we were able to resolve individual compounds within humic and fulvic acid mixtures(More)
The acetylation of the NH2-terminal tail of histone H4 by type B histone acetyltransferases (HATs) is involved in the process of chromatin assembly. Histone H4 associated with a nuclear type B HAT complex contains modifications in its globular core domain as well. In particular, acetylation was found at lysine 91. A mutation that alters this residue, which(More)
The core histones are the primary protein component of chromatin, which is responsible for the packaging of eukaryotic DNA. The NH(2)-terminal tail domains of the core histones are the sites of numerous post-translational modifications that have been shown to play an important role in the regulation of chromatin structure. In this study, we discuss the(More)
A new database search algorithm has been developed to identify disulfide-linked peptides in tandem MS data sets. The algorithm is included in the newly developed tandem MS database search program, MassMatrix. The algorithm exploits the probabilistic scoring model in MassMatrix to achieve identification of disulfide bonds in proteins and peptides. Proteins(More)
A new database search algorithm has been developed for identification of intact cross-links in proteins and peptides from tandem mass spectrometric data. Using this algorithm, intact cross-links can be identified and characterized in proteins and peptides with high confidence. The algorithm was tested using BS(3) (bis[sulfosuccinimidyl] suberate)(More)
The acetylated isoforms of histone H4 from mouse lymphosarcoma cells treated with HDAC inhibitors trichostatin A (TSA) and depsipeptide (DDP) were separated by acetic acid urea-polyacrylamide gel electrophoresis (AU-PAGE), in-gel digested, and analyzed by matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid(More)
Histone H1 is commonly used to assay kinase activity in vitro. As many promising targeted therapies affect kinase activity of specific enzymes involved in cancer transformation, H1 phosphorylation can serve as potential pharmacodynamic marker for drug activity within the cell. In this study we utilized a phosphoproteomic workflow to characterize histone H1(More)