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      The enzymes of human diphosphoinositol polyphosphate metabolism

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          Abstract

          Diphospho- myo-inositol polyphosphates have many roles to play, including roles in apoptosis, vesicle trafficking, the response of cells to stress, the regulation of telomere length and DNA damage repair, and inhibition of the cyclin-dependent kinase Pho85 system that monitors phosphate levels. This review focuses on the three classes of enzymes involved in the metabolism of these compounds: inositol hexakisphosphate kinases, inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinases and diphosphoinositol polyphosphate phosphohydrolases. However, these enzymes have roles beyond being mere catalysts, and their interactions with other proteins have cellular consequences. Through their interactions, the three inositol hexakisphosphate kinases have roles in exocytosis, diabetes, the response to infection, and apoptosis. The two inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinases influence the cellular response to phosphatidylinositol (3,4,5)-trisphosphate and the migration of pleckstrin homology domain-containing proteins to the plasma membrane. The five diphosphoinositol polyphosphate phosphohydrolases interact with ribosomal proteins and transcription factors, as well as proteins involved in membrane trafficking, exocytosis, ubiquitination and the proteasomal degradation of target proteins. Possible directions for future research aiming to determine the roles of these enzymes are highlighted.

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          A probability-based approach for high-throughput protein phosphorylation analysis and site localization.

          Data analysis and interpretation remain major logistical challenges when attempting to identify large numbers of protein phosphorylation sites by nanoscale reverse-phase liquid chromatography/tandem mass spectrometry (LC-MS/MS) (Supplementary Figure 1 online). In this report we address challenges that are often only addressable by laborious manual validation, including data set error, data set sensitivity and phosphorylation site localization. We provide a large-scale phosphorylation data set with a measured error rate as determined by the target-decoy approach, we demonstrate an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs), and we present a probability-based score, the Ascore, that measures the probability of correct phosphorylation site localization based on the presence and intensity of site-determining ions in MS/MS spectra. We applied our methods in a fully automated fashion to nocodazole-arrested HeLa cell lysate where we identified 1,761 nonredundant phosphorylation sites from 491 proteins with a peptide false-positive rate of 1.3%.
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            The IntAct molecular interaction database in 2012

            IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. Two levels of curation are now available within the database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported. As from September 2011, IntAct contains approximately 275 000 curated binary interaction evidences from over 5000 publications. The IntAct website has been improved to enhance the search process and in particular the graphical display of the results. New data download formats are also available, which will facilitate the inclusion of IntAct's data in the Semantic Web. IntAct is an active contributor to the IMEx consortium (http://www.imexconsortium.org). IntAct source code and data are freely available at http://www.ebi.ac.uk/intact.
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              TOR, a Central Controller of Cell Growth

              Cell, 103(2), 253-262
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                Author and article information

                Journal
                FEBS J
                FEBS J
                febs
                The Febs Journal
                BlackWell Publishing Ltd (Oxford, UK )
                1742-464X
                1742-4658
                January 2014
                05 November 2013
                : 281
                : 1
                : 14-33
                Affiliations
                Department of Pharmacy & Pharmacology, University of Bath UK
                Author notes
                B. V. L. Potter, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK Fax: +44 (0)1225 386114 Tel: +44 (0)1225 386639 E-mail: b.v.l.potter@ 123456bath.ac.uk
                Article
                10.1111/febs.12575
                4063336
                24152294
                a0b6309a-2ee0-4f69-9959-4e0598dcc030
                © 2013 The Authors. FEBS Journal published by John Wiley & Sons Ltd on behalf of FEBS.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 25 June 2013
                : 10 September 2013
                : 15 October 2013
                Categories
                Review Articles

                Molecular biology
                diphosphoinositol polyphosphate phosphohydrolase,inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase,inositol hexakisphosphate kinase,inositol pyrophosphate

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