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  • 1
    Language: English
    In: Analytical chemistry, 06 October 2015, Vol.87(19), pp.9939-45
    Description: We introduce fragment ion patchwork quantification as a new mass spectrometry-based approach for the highly accurate quantification of site-specific acetylation degrees. This method combines (13)C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Acetylation degrees are determined from the isotope patterns of acetylated b and y ions. We show that this approach allows to determine site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei. In addition, we demonstrate how this approach can be used to identify substrate sites of histone acetyltransferases.
    Keywords: Histones -- Chemistry ; Lysine -- Analysis ; Trypanosoma Brucei Brucei -- Chemistry
    ISSN: 00032700
    E-ISSN: 1520-6882
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  • 2
    Language: English
    In: Analytical Chemistry, Oct 6, 2015, Vol.87(19), p.9939(7)
    Description: The article introduces fragment ion patchwork quantification as a new mass spectrometry-based approach for the highly accurate quantification of site-specific acetylation degrees. This method merges 13C1-acetyl derivatization on the protein level, proteolysis by low-specificity proteases and quantification on the fragment ion level. Moreover, it is shown that this method enables determination of site-specific acetylation degrees of all lysine residues for all core histones of Trypanosoma brucei.
    Keywords: Acetylation – Analysis ; Mass Spectrometry – Usage ; Patchwork – Research
    ISSN: 0003-2700
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Journal of medicinal chemistry, 25 May 2017, Vol.60(10), pp.4147-4160
    Description: Heat shock transcription factor 1 (HSF1) has been identified as a therapeutic target for pharmacological treatment of multiple myeloma (MM). However, direct therapeutic targeting of HSF1 function seems to be difficult due to the shortage of clinically suitable pharmacological inhibitors. We utilized the Ugi multicomponent reaction to create a small but smart library of α-acyl aminocarboxamides and evaluated their ability to suppress heat shock response (HSR) in MM cells. Using the INA-6 cell line as the MM model and the strictly HSF1-dependent HSP72 induction as a HSR model, we identified potential HSF1 inhibitors. Mass spectrometry-based affinity capture experiments with biotin-linked derivatives revealed a number of target proteins and complexes, which exhibit an armadillo domain. Also, four members of the tumor-promoting and HSF1-associated phosphatidylinositol 3-kinase-related kinase (PIKK) family were identified. The antitumor activity was evaluated, showing that treatment with the anti-HSF1 compounds strongly induced apoptotic cell death in MM cells.
    Keywords: Antineoplastic Agents -- Chemistry ; Apoptosis -- Drug Effects ; DNA-Binding Proteins -- Antagonists & Inhibitors ; Multiple Myeloma -- Drug Therapy ; Phosphatidylinositol 3-Kinases -- Metabolism ; Transcription Factors -- Antagonists & Inhibitors
    ISSN: 00222623
    E-ISSN: 1520-4804
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  • 4
    Language: English
    In: Analytical chemistry, 01 October 2007, Vol.79(19), pp.7439-49
    Description: We have developed novel scoring schemes for the identification of (phospho)peptides (PeptideScore) and for pinpointing phosphorylation sites (PhosphoSiteScore) using MS/MS data. These scoring schemes have been developed for the in-depth analysis of individual phosphoproteins, not for large-scale phosphoproteomic-type data. The scoring schemes are implemented into the new software tool Phosm, which provides a concise and comprehensive presentation of the results. For development and evaluation of these schemes, we have analyzed approximately 500 phosphopeptide MS/MS spectra, most of them nontryptic peptides. The novel scoring schemes turned out to be very powerful, even with CID MS/MS spectra of very low quality. Many phosphopeptides and phosphorylation sites that remained unassigned in our LC-MS/MS data sets with Mascot could be identified with Phosm. Especially the number of identified multiply phosphorylated peptides could be significantly increased. The applied scoring parameters are described, and the scoring for several selected examples of phosphopeptides is discussed in detail. Furthermore, a new and simple nomenclature for all types of phosphorylated fragment ions is introduced in this publication.
    Keywords: Phosphoproteins -- Metabolism ; Tandem Mass Spectrometry -- Methods
    ISSN: 0003-2700
    E-ISSN: 15206882
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  • 5
    Language: English
    In: Molecular & cellular proteomics : MCP, August 2011, Vol.10(8), pp.O110.007450
    Description: Recent technological advances have made it possible to identify and quantify thousands of proteins in a single proteomics experiment. As a result of these developments, the analysis of data has become the bottleneck of proteomics experiment. To provide the proteomics community with a user-friendly platform for comprehensive analysis, inspection and visualization of quantitative proteomics data we developed the Graphical Proteomics Data Explorer (GProX)(1). The program requires no special bioinformatics training, as all functions of GProX are accessible within its graphical user-friendly interface which will be intuitive to most users. Basic features facilitate the uncomplicated management and organization of large data sets and complex experimental setups as well as the inspection and graphical plotting of quantitative data. These are complemented by readily available high-level analysis options such as database querying, clustering based on abundance ratios, feature enrichment tests for e.g. GO terms and pathway analysis tools. A number of plotting options for visualization of quantitative proteomics data is available and most analysis functions in GProX create customizable high quality graphical displays in both vector and bitmap formats. The generic import requirements allow data originating from essentially all mass spectrometry platforms, quantitation strategies and software to be analyzed in the program. GProX represents a powerful approach to proteomics data analysis providing proteomics experimenters with a toolbox for bioinformatics analysis of quantitative proteomics data. The program is released as open-source and can be freely downloaded from the project webpage at http://gprox.sourceforge.net.
    Keywords: Software
    ISSN: 15359476
    E-ISSN: 1535-9484
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  • 6
    In: Scientific Reports, 2017, Vol.7
    Description: Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15 N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis.
    Keywords: Rrna ; RNA Polymerase ; Transcription Initiation ; Histones ; Lysis ; Chaperones ; Mrna Turnover ; Chromatin Remodeling ; Transcription Factors ; RNA Processing ; Yeast ; Splicing ; DNA-Directed RNA Polymerase ; Chromatin ; Proteins ; Protein Interaction;
    E-ISSN: 2045-2322
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  • 7
    Language: English
    In: Analytical Chemistry, August 15, 2005, Vol.77(16), p.5243(8)
    Description: We have developed a multi-protease approach that allows sensitive and comprehensive mapping of protein phosphorylation sites. The combined application of the low-specificity proteases elastase, proteinase K, and thermolysin in addition to trypsin results in high sequence coverage, a prerequisite for comprehensive phosphorylation site mapping. Phosphopeptide enrichment is performed with the recently introduced phosphopeptide affinity material titansphere. We have optimized the selectivity of the phosphopeptide enrichment with titansphere, without compromising the high recovery rate of ~90%. Phosphopeptide-enriched fractions are analyzed with a highly sensitive nanoLC-MS/MS system using a 25-[micro]m-i.d. reversed-phase column, operated at a flow rate of 25 nL/min. The new approach was applied to the murine circadian protein period 2 (mPER2). A total of 21 phosphorylation sites of mPER2 have been detected by the multi-protease approach, whereas only 6 phosphorylation sites were identified using solely trypsin. Titansphere proved to be well suited for the enrichment of a large variety of phosphopeptides, including peptides carrying two, three, or four phosphorylated residues, as well as phosphopeptides containing more basic than acidic amino acids.
    Keywords: Phosphorylation -- Research ; Mass Spectrometry -- Usage ; Proteases -- Research
    ISSN: 0003-2700
    E-ISSN: 15206882
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  • 8
    Language: English
    In: Archives of Toxicology, 2018, Vol.92(2), pp.995-1014
    Description: Ochratoxin A (OTA) is a potent renal carcinogen but its mechanism has not been fully resolved. In vitro and in vivo gene expression studies consistently revealed down-regulation of gene expression as the predominant transcriptional response to OTA. Based on the importance of specific histone acetylation marks in regulating gene transcription and our recent finding that OTA inhibits histone acetyltransferases (HATs), leading to loss of acetylation of histones and non-histone proteins, we hypothesized that OTA-mediated repression of gene expression may be causally linked to HAT inhibition and loss of histone acetylation. In this study, we used a novel mass spectrometry approach employing chemical 13 C-acetylation of unmodified lysine residues for quantification of post-translational acetylation sites to identify site-specific alterations in histone acetylation in human kidney epithelial cells (HK-2) exposed to OTA. These results showed OTA-mediated hypoacetylation at almost all lysine residues of core histones, including loss of acetylation at H3K9 and H3K14, which are hallmarks of gene activation. ChIP-qPCR used to establish a possible link between H3K9 or H3K14 hypoacetylation and OTA-mediated down-regulation of selected genes ( AMIGO2 , CLASP2 , CTNND1 ) confirmed OTA-mediated H3K9 hypoacetylation at promoter regions of these genes. Integrated analysis of OTA-mediated genome-wide changes in H3K9 acetylation identified by ChIP-Seq with published gene expression data further demonstrated that among OTA-responsive genes almost 80% of hypoacetylated genes were down-regulated, thus confirming an association between H3K9 acetylation status and gene expression of these genes. However, only 7% of OTA repressed genes showed loss of H3K9 acetylation within promoter regions. Interestingly, however, GO analysis and functional enrichment of down-regulated genes showing loss of H3K9 acetylation at their respective promoter regions revealed enrichment of genes involved in the regulation of transcription, including a number of transcription factors that are predicted to directly or indirectly regulate the expression of 98% of OTA repressed genes. Thus, it is possible that histone acetylation changes in a fairly small set of genes but with key function in transcriptional regulation may trigger a cascade of events that may lead to overall repression of gene expression. Taken together, our data provide evidence for a mechanistic link between loss of H3K9 acetylation as a consequence of OTA-mediated inhibition of HATs and repression of gene expression by OTA, thereby affecting cellular processes critical to tumorigenesis.
    Keywords: Ochratoxin A ; Histone hypoacetylation ; Repression of gene expression ; Renal carcinogenicity
    ISSN: 0340-5761
    E-ISSN: 1432-0738
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  • 9
    In: Journal of Comparative Neurology, 01 March 2017, Vol.525(4), pp.901-918
    Description: desert ants exhibit an age‐related polyethism, with ants performing tasks in the dark nest for the first ∼4 weeks of their adult life before they switch to visually based long‐distance navigation to forage. Although behavioral and sensory aspects of this transition have been studied, the internal factors triggering the behavioral changes are largely unknown. We suggest the neuropeptide families allatostatin A (AstA), allatotropin (AT), short neuropeptide F (sNPF), and tachykinin (TK) as potential candidates. Based on a neuropeptidomic analysis in , nano‐LC‐ESI MS/MS was used to identify these neuropeptides biochemically in . Furthermore, we show that all identified peptide families are present in the central brain and ventral ganglia of whereas in the retrocerebral complex only sNPF could be detected. Immunofluorescence staining against AstA, AT, and TK in the brain revealed arborizations of AstA‐ and TK‐positive neurons in primary sensory processing centers and higher order integration centers, whereas AT immunoreactivity was restricted to the central complex, the antennal mechanosensory and motor center, and the protocerebrum. For artificially dark‐kept ants, we found that TK distribution changed markedly in the central complex from days 1 and 7 to day 14 after eclosion. Based on functional studies in , this age‐related variation of TK is suggestive of a modulatory role in locomotion behavior in . We conclude that the general distribution and age‐related changes in neuropeptides indicate a modulatory role in sensory input regions and higher order processing centers in the desert ant brain. J. Comp. Neurol. 525:901–918, 2017. © 2016 Wiley Periodicals, Inc. Neuropeptides are known to regulate animal physiology and behavior. The present study uses mass spectrometry and immunohistology to analyze the neuropeptide families allatostatin A, allatotropin, short neuropeptide F, and tachykinin, which we deem regulatory for behavioral transitions in the desert ant .
    Keywords: Allatostatin A ; Allatotropin ; Short Neuropeptide F ; Tachykinin ; Division Of Labor ; Rrid:Ab_2313972 ; Rrid:Ab_2315469 ; Rrid:Ab_2315426
    ISSN: 0021-9967
    E-ISSN: 1096-9861
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  • 10
    In: The Journal of Bacteriology, 2009, Vol. 191(17), p.5342
    Description: Organisms coordinate biological activities into daily cycles using an internal circadian clock. The circadian oscillator proteins KaiA, KaiB, and KaiC are widely believed to underlie 24-h oscillations of gene expression in cyanobacteria. However, a group of very abundant cyanobacteria, namely, marine Prochlorococcus species, lost the third oscillator component, KaiA, during evolution. We demonstrate here that the remaining Kai proteins fulfill their known biochemical functions, although KaiC is hyperphosphorylated by default in this system. These data provide biochemical support for the observed evolutionary reduction of the clock locus in Prochlorococcus and are consistent with a model in which a mechanism that is less robust than the well-characterized KaiABC protein clock of Synechococcus is sufficient for biological timing in the very stable environment that Prochlorococcus inhabits. [PUBLICATION ]
    Keywords: Bacteria ; Bacteriology ; Biochemistry ; Circadian Rhythm ; Proteins;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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