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phosphoproteomics

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https://www.readbyqxmd.com/read/28818855/paradigm-of-biased-par1-protease-activated-receptor-1-activation-and-inhibition-in-endothelial-cells-dissected-by-phosphoproteomics
#1
Bart L van den Eshof, Arie J Hoogendijk, Pelle J Simpson, Floris P J van Alphen, Sara Zanivan, Koen Mertens, Alexander B Meijer, Maartje van den Biggelaar
OBJECTIVE: Thrombin is the key serine protease of the coagulation cascade and mediates cellular responses by activation of PARs (protease-activated receptors). The predominant thrombin receptor is PAR1, and in endothelial cells (ECs), thrombin dynamically regulates a plethora of phosphorylation events. However, it has remained unclear whether thrombin signaling is exclusively mediated through PAR1. Furthermore, mechanistic insight into activation and inhibition of PAR1-mediated EC signaling is lacking...
August 17, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28816646/chronic-cigarette-smoke-mediated-global-changes-in-lung-mucoepidermoid-cells-a-phosphoproteomic-analysis
#2
Hitendra S Solanki, Jayshree Advani, Aafaque Ahmad Khan, Aneesha Radhakrishnan, Nandini A Sahasrabuddhe, Sneha M Pinto, Xiaofei Chang, Thottethodi Subrahmanya Keshava Prasad, Premendu Prakash Mathur, David Sidransky, Harsha Gowda, Aditi Chatterjee
Proteomics analysis of chronic cigarette smoke exposure is a rapidly emerging postgenomics research field. While smoking is a major cause of lung cancer, functional studies using proteomics approaches could enrich our mechanistic understanding of the elusive lung cancer global molecular signaling and cigarette smoke relationship. We report in this study on a stable isotope labeling by amino acids in cell culture-based quantitative phosphoproteomic analysis of a human lung mucoepidermoid carcinoma cell line, H292 cells, chronically exposed to cigarette smoke...
August 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28808226/atr-inhibition-facilitates-targeting-of-leukemia-dependence-on-convergent-nucleotide-biosynthetic-pathways
#3
Thuc M Le, Soumya Poddar, Joseph R Capri, Evan R Abt, Woosuk Kim, Liu Wei, Nhu T Uong, Chloe M Cheng, Daniel Braas, Mina Nikanjam, Peter Rix, Daria Merkurjev, Jesse Zaretsky, Harley I Kornblum, Antoni Ribas, Harvey R Herschman, Julian Whitelegge, Kym F Faull, Timothy R Donahue, Johannes Czernin, Caius G Radu
Leukemia cells rely on two nucleotide biosynthetic pathways, de novo and salvage, to produce dNTPs for DNA replication. Here, using metabolomic, proteomic, and phosphoproteomic approaches, we show that inhibition of the replication stress sensing kinase ataxia telangiectasia and Rad3-related protein (ATR) reduces the output of both de novo and salvage pathways by regulating the activity of their respective rate-limiting enzymes, ribonucleotide reductase (RNR) and deoxycytidine kinase (dCK), via distinct molecular mechanisms...
August 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28808029/elucidating-crosstalk-mechanisms-between-phosphorylation-and-o-glcnacylation
#4
Aneika C Leney, Dris El Atmioui, Wei Wu, Huib Ovaa, Albert J R Heck
Proteins can be modified by multiple posttranslational modifications (PTMs), creating a PTM code that controls the function of proteins in space and time. Unraveling this complex PTM code is one of the great challenges in molecular biology. Here, using mass spectrometry-based assays, we focus on the most common PTMs-phosphorylation and O-GlcNAcylation-and investigate how they affect each other. We demonstrate two generic crosstalk mechanisms. First, we define a frequently occurring, very specific and stringent phosphorylation/O-GlcNAcylation interplay motif, (pSp/T)P(V/A/T)(gS/gT), whereby phosphorylation strongly inhibits O-GlcNAcylation...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28803361/toxoplasma-gondii-and-neospora-caninum-induce-different-host-cell-responses-at-proteome-wide-phosphorylation-events-a-step-forward-for-uncovering-the-biological-differences-between-these-closely-related-parasites
#5
Mariwan M M Al-Bajalan, Dong Xia, Stuart Armstrong, Nadine Randle, Jonathan M Wastling
Toxoplasma gondii and Neospora caninum are closely related intracellular protozoan parasites and tissue cyst-forming Coccidia of the phylum Apicomplexa. There are remarkable similarities between the morphology, genomes and transcriptomes of both parasites. Toxoplasma is zoonotic, with a wide host range and is mainly transmitted horizontally between its definitive host, the cat, and its intermediate hosts. Neospora causes disease within a narrow host range and with reduced virulence potential to the hosts. The dog is the definitive host of Neospora and its epidemiology in cattle mainly depends on vertical transmission...
August 12, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28796482/a-sensitive-robust-and-cost-effective-approach-for-tyrosine-phosphoproteome-analysis
#6
Mingming Dong, Yangyang Bian, Yan Wang, Jing Dong, Yating Yao, Zhenzhen Deng, Hongqiang Qin, Hanfa Zou, Mingliang Ye
Albeit much less abundant than Ser/Thr phosphorylation (pSer/pThr), Tyr phosphorylation (pTyr) is considered as a hallmark in cellular signal transduction. However, its analysis at the proteome level remains challenging. The conventional immunopurification (IP) approach using antibodies specific to pTyr sites is known to have low sensitivity, poor reproducibility and high cost. Our recent study indicated that SH2 domain-derived pTyr-superbinder is a good replacement of pTyr antibody for the specific enrichment of pTyr peptides for phosphoproteomics analysis...
August 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28795574/molecularly-imprinted-porous-monolithic-materials-from-melamine-formaldehyde-for-selective-trapping-of-phosphopeptides
#7
Mingquan Liu, Tri Minh Tran, Ahmed Awad Abbas Elhaj, Silje Bøen Torsetnes, Ole Nørregaard Jensen, Börje Sellergren, Knut Irgum
Thirty-five melamine-formaldehyde (MF) monolithic materials with bimodal pore distributions were synthesized in fused silica capillaries by catalyst-free polycondensation, starting with an aqueous MF precondensate, using acetonitrile as macroporogen and a variety of aliphatic polyethers and triblock copolymeric surfactants as porogens and mesoporogens, respectively. By varying the prepolymer composition and the type and molecular weights of the polymeric porogen components, a library of porous monolithic materials were produced, covering a range of meso- and macroporous properties...
August 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28794502/proteomics-phosphoproteomics-of-left-ventricular-biopsies-from-patients-with-surgical-coronary-revascularization-and-pigs-with-coronary-occlusion-reperfusion-remote-ischemic-preconditioning
#8
Nilgün Gedik, Marcus Krüger, Matthias Thielmann, Eva Kottenberg, Andreas Skyschally, Ulrich H Frey, Elke Cario, Jürgen Peters, Heinz Jakob, Gerd Heusch, Petra Kleinbongard
Remote ischemic preconditioning (RIPC) by repeated brief cycles of limb ischemia/reperfusion reduces myocardial ischemia/reperfusion injury. In left ventricular (LV) biopsies from patients undergoing coronary artery bypass grafting (CABG), only the activation of signal transducer and activator of transcription 5 was associated with RIPC's cardioprotection. We have now used an unbiased, non-hypothesis-driven proteomics and phosphoproteomics approach to analyze LV biopsies from patients undergoing CABG and from pigs undergoing coronary occlusion/reperfusion without (sham) and with RIPC...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28768720/angiotensin-ii-regulates-phosphorylation-of-actin-associated-proteins-in-human-podocytes
#9
Laura K Schenk, Annika Möller-Kerutt, Rafael Klosowski, Dirk Wolters, Elisabeth Schaffner-Reckinger, Thomas Weide, Hermann Pavenstädt, Beate Vollenbröker
Within the kidney, angiotensin II (AngII) targets different cell types in the vasculature, tubuli, and glomeruli. An important part of the renal filtration barrier is composed of podocytes with their actin-rich foot processes. In this study, we used stable isotope labeling with amino acids in cell culture coupled to mass spectrometry to characterize relative changes in the phosphoproteome of human podocytes in response to short-term treatment with AngII. In 4 replicates, we identified a total of 17,956 peptides that were traceable to 2081 distinct proteins...
August 2, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28761071/phosphopredict-a-bioinformatics-tool-for-prediction-of-human-kinase-specific-phosphorylation-substrates-and-sites-by-integrating-heterogeneous-feature-selection
#10
Jiangning Song, Huilin Wang, Jiawei Wang, André Leier, Tatiana Marquez-Lago, Bingjiao Yang, Ziding Zhang, Tatsuya Akutsu, Geoffrey I Webb, Roger J Daly
Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes. In silico methods for phosphorylation site prediction can provide a useful and complementary strategy for complete phosphoproteome annotation. Here, we present a novel bioinformatics tool, PhosphoPredict, that combines protein sequence and functional features to predict kinase-specific substrates and their associated phosphorylation sites for 12 human kinases and kinase families, including ATM, CDKs, GSK-3, MAPKs, PKA, PKB, PKC, and SRC...
July 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747907/membrane-phosphoproteomics-of-yeast-early-response-to-acetic-acid-role-of-hrk1-kinase-and-lipid-biosynthetic-pathways-in-particular-sphingolipids
#11
Joana F Guerreiro, Nuno P Mira, Aline X S Santos, Howard Riezman, Isabel Sá-Correia
Saccharomyces cerevisiae response and tolerance to acetic acid is critical in industrial biotechnology and in acidic food and beverages preservation. The HRK1 gene, encoding a protein kinase of unknown function belonging to the "Npr1-family" of kinases known to be involved in the regulation of plasma membrane transporters, is an important determinant of acetic acid tolerance. This study was performed to identify the alterations occurring in yeast membrane phosphoproteome profile during the adaptive early response to acetic acid stress (following 1 h of exposure to a sub-lethal inhibitory concentration; 50 mM at pH 4...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28741359/evaluation-of-parameters-for-confident-phosphorylation-site-localization-using-an-orbitrap-fusion-tribrid-mass-spectrometer
#12
Samantha Ferries, Simon Perkins, Philip J Brownridge, Amy Campbell, Patrick A Eyers, Andrew R Jones, Claire E Eyers
Confident identification of sites of protein phosphorylation by mass spectrometry (MS) is essential to advance understanding of phosphorylation-mediated signaling events. However, development of novel instrumentation requires that methods for MS data acquisition and its interrogation be evaluated and optimized for high throughput phosphoproteomics. Here, we compare and contrast eight MS acquisition methods on the novel tribrid Orbitrap Fusion MS platform, using both a synthetic phosphopeptide library and a complex phosphopeptide-enriched cell lysate...
July 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28735398/phosphoproteomics-analysis-for-probing-plant-stress-tolerance
#13
Christof Rampitsch
Protein phosphorylation is a key signaling mechanism during the plant biotic and abiotic stress response. Signaling cascades communicate between the cell surface, where the stress is perceived, and the nucleus, where a response can be enacted. Many of these signals involve the specific, transient phosphorylation of proteins by kinases, a signal which is usually amplified through cascades. The advent of high-throughput phosphoproteomics, pioneered mainly in yeast and mammalian cells, has made it possible to discover novel phosphorylation events rapidly and efficiently in a data-dependent manner and this has greatly enlarged our understanding of the plant's response to stress...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28731282/altered-signaling-associated-with-chronic-arsenic-exposure-in-human-skin-keratinocytes
#14
Sartaj Ahmad Mir, Santosh Renuse, Gajanan Sathe, Aafaque Ahmad Khan, Arun H Patil, Vishalakshi Nanjappa, Firdous Ahmad Bhat, T S Keshava Prasad, Ashok K Giri, Aditi Chatterjee, Harsha Gowda
Modulation of signaling pathways upon chronic arsenic exposure remains poorly studied. Here we carried out SILAC-based quantitative phosphoproteomics analysis to dissect the signaling induced upon chronic arsenic exposure in human skin keratinocyte cell line, HaCaT. We identified 4,171 unique phosphosites derived from 2,000 proteins. We observed differential phosphorylation of 406 phosphosites (2-fold) corresponding to 305 proteins. Several pathways involved in cytoskeleton maintenance and organization were found to be significantly enriched (p<0...
July 21, 2017: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/28730489/identification-of-plant-kinase-substrates-based-on-kinase-assay-linked-phosphoproteomics
#15
Chuan-Chih Hsu, Justine V Arrington, Liang Xue, W Andy Tao
Protein phosphorylation is one of the key events in the regulation of plant physiological responses to diverse environmental stimuli. As crucial regulators of phosphorylation, protein kinases have been linked to the control of seed germination, flowering, and stress responses. Identifying downstream substrates of kinases is important for dissecting kinase-substrate networks as well as delineating the underlying defense mechanisms in response to extracellular stimulation. Despite the fact that thousands of kinase-substrate networks have been identified in mammalian cells, the downstream substrates of important plant kinases are still elusive...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#16
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730486/phosphoproteomic-analysis-of-isolated-mitochondria-in-yeast
#17
Margaux Renvoisé, Ludovic Bonhomme, Marlène Davanture, Michel Zivy, Claire Lemaire
Mitochondria play a central role in cellular energy metabolism and cell death. Deregulation of mitochondrial functions is associated with several human pathologies (neurodegenerative diseases, neuromuscular diseases, type II diabetes, obesity, cancer). The steadily increasing number of identified mitochondrial phosphoproteins, kinases, and phosphatases in recent years suggests that reversible protein phosphorylation plays an important part in the control of mitochondrial processes. In addition, many mitochondrial phosphoproteins probably still remain to be identified, considering that 30% of proteins are expected to be phosphorylated in eukaryotes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730485/targeted-analysis-of-phosphotyrosine-signaling-by-multiple-reaction-monitoring-mass-spectrometry
#18
Leo S Payne, Paul H Huang
Phosphoproteomics is an important tool for the unbiased investigation of signaling network activation and has particular application to unraveling aberrant signaling driving cancer progression. However, validating the behavior of specific phosphosites across multiple experimental conditions remains challenging, due to limitations inherent in discovery-based proteomic workflows and the limited availability of high-quality antibodies required for alternative, immunoaffinity-based methods. Targeted phosphoproteomics enables specific phosphosites to be quantified reproducibly across multiple experimental conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730483/characterization-of-the-phospho-adhesome-by-mass-spectrometry-based-proteomics
#19
Joseph Robertson, Jonathan D Humphries, Nikki R Paul, Stacey Warwood, David Knight, Adam Byron, Martin J Humphries
Integrin adhesion receptors engage with their extracellular matrix (ECM) ligands, initiating intracellular signaling pathways that regulate a range of fundamental cell functions. Protein kinases and phosphatases play an integral role in integrin adhesion-mediated signaling. However, until recently, knowledge of the phosphorylation sites regulated downstream of integrin ligation was limited to candidate-based approaches and did not support a system-level understanding of the molecular mechanisms through which ECM engagement influences cell behavior...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730481/label-free-phosphoproteomic-approach-for-kinase-signaling-analysis
#20
Edmund Wilkes, Pedro R Cutillas
Phosphoproteomics is a powerful platform for the unbiased profiling of kinase-driven signaling pathways. Quantitation of phosphorylation can be performed by means of either labeling or label-free mass spectrometry (MS) methods. Because of their simplicity and universality, label-free methodology is gaining acceptance and popularity in molecular biology research. Analytical workflows for label-free quantification of phosphorylation, however, need to overcome several hurdles for the technique to be accurate and precise...
2017: Methods in Molecular Biology
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