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https://www.readbyqxmd.com/read/28345880/detecting-proteins-glycosylation-by-a-homogeneous-reaction-system-with-zwitterionic-gold-nanoclusters
#1
Jinan Li, Jing Liu, Zheyi Liu, Yuan Tan, Xiaoyan Liu, Fangjun Wang
Homogeneous gold nanoclusters (Au NCs) have been widely utilized in drug delivery, chemical sensing, bioassays and bio-labeling due to their unique physical and chemical properties. However, little attention has been paid to their application in detecting protein post-translational modifications. Herein, we describe development of a homogeneous reaction system with water-soluble zwitterionic Au NCs to capture glycopeptides from complex biological samples. The unique characteristics of Au NCs, such as their molecular-like properties, the excellent homogeneity in aqueous solution, the organic solvent respon-sive precipitation, and the easy preparation in only 4...
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345864/triple-stage-mass-spectrometry-unravels-the-heterogeneity-of-an-endogenous-protein-complex
#2
Gili Ben-Nissan, Mikhail E Belov, David Morgenstern, Yishai Levin, Orly Dym, Galina Arkind, Carni Lipson, Alexander A Makarov, Michal Sharon
The way we perceive protein complexes is changing. What were once thought to be uniform entities may actually represent an ensemble of different assemblies with distinct functions and regulation. This increased complexity is enabled by the variety of protein diversification mechanisms that exist at every step of the protein biosynthesis pathway, such as alternative splicing and post transcriptional and translational modifications. The resulting variation in subunits can generate compositionally distinct protein assemblies...
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345603/pja2-ubiquitinates-the-hiv-1-tat-protein-with-atypical-chain-linkages-to-activate-viral-transcription
#3
Tyler B Faust, Yang Li, Gwendolyn M Jang, Jeffrey R Johnson, Shumin Yang, Amit Weiss, Nevan J Krogan, Alan D Frankel
Transcription complexes that assemble at the HIV-1 promoter efficiently initiate transcription but generate paused RNA polymerase II downstream from the start site. The virally encoded Tat protein hijacks positive transcription elongation factor b (P-TEFb) to phosphorylate and activate this paused polymerase. In addition, Tat undergoes a series of reversible post-translational modifications that regulate distinct steps of the transcription cycle. To identify additional functionally important Tat cofactors, we performed RNAi knockdowns of sixteen previously identified Tat interactors and found that a novel E3 ligase, PJA2, ubiquitinates Tat in a non-degradative manner and specifically regulates the step of HIV transcription elongation...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28345137/a-comparative-analysis-of-phosphoproteome-in-ovine-muscle-at-early-postmortem-in-relationship-to-tenderness-%C3%A2
#4
Xin Li, Lijuan Chen, Fan He, Meng Li, Qingwu Shen, Dequan Zhang
BACKGROUND: Tenderness is considered to be the most important quality characteristic of meat as it is the main cause of unacceptability of meat. Post-translational modification regulates protein functions that involve in postmortem changes in muscle and meat quality formation. Specifically, phosphorylation was proved to regulate postmortem glycolytic rates and meat tenderization. However, the relationship between protein phosphorylation and meat tenderness remains unclear. This study examined the phosphoproteomes found in ovine muscle with different degrees of tenderness over time (at 0...
March 26, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28344560/nitric-oxide-has-a-concentration-dependent-effect-on-the-cell-cycle-acting-via-ein2-in-arabidopsis-thaliana-cultured-cells
#5
Galina V Novikova, Luis A J Mur, Alexander V Nosov, Artem A Fomenkov, Kirill S Mironov, Anna S Mamaeva, Evgeny S Shilov, Victor Y Rakitin, Michael A Hall
Ethylene is known to influence the cell cycle (CC) via poorly characterized roles whilst nitric oxide (NO) has well-established roles in the animal CC but analogous role(s) have not been reported for plants. As NO and ethylene signaling events often interact we examined their role in CC in cultured cells derived from Arabidopsis thaliana wild-type (Col-0) plants and from ethylene-insensitive mutant ein2-1 plants. Both NO and ethylene were produced mainly during the first 5 days of the sub-cultivation period corresponding to the period of active cell division...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28344354/hdac1-3-inhibitor-ms-275-enhances-il10-expression-in-raw264-7-macrophages-and-reduces-cigarette-smoke-induced-airway-inflammation-in-mice
#6
Niek G J Leus, Thea van den Bosch, Petra E van der Wouden, Kim Krist, Maria E Ourailidou, Nikolaos Eleftheriadis, Loes E M Kistemaker, Sophie Bos, Rutger A F Gjaltema, Solomon A Mekonnen, Rainer Bischoff, Reinoud Gosens, Hidde J Haisma, Frank J Dekker
Chronic obstructive pulmonary disease (COPD) constitutes a major health burden. Studying underlying molecular mechanisms could lead to new therapeutic targets. Macrophages are orchestrators of COPD, by releasing pro-inflammatory cytokines. This process relies on transcription factors such as NF-κB, among others. NF-κB is regulated by lysine acetylation; a post-translational modification installed by histone acetyltransferases and removed by histone deacetylases (HDACs). We hypothesized that small molecule HDAC inhibitors (HDACi) targeting class I HDACs members that can regulate NF-κB could attenuate inflammatory responses in COPD via modulation of the NF-κB signaling output...
March 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28342847/na-k-atpase-interaction-with-methylglyoxal-as-reactive-metabolic-side-product
#7
Marika Svrckova, Martina Zatloukalova, Petra Dvorakova, Dominika Coufalova, David Novak, Lenka Hernychova, Jan Vacek
Proteins are subject to oxidative modification and the formation of adducts with a broad spectrum of reactive species via enzymatic and non-enzymatic mechanisms. Here we report that in vitro non-enzymatic methylglyoxal (MGO) binding causes the inhibition and formation of MGO advanced glycation end-products (MAGEs) in Na(+)/K(+)-ATPase (NKA). Concretely, MGO adducts with NKA amino acid residues (mainly Arg) and N(ε)-(carboxymethyl)lysine (CML) formation were found. MGO is not only an inhibitor for solubilized NKA (IC50 = 91±16 μM), but also for reconstituted NKA in the lipid bilayer environment, which was clearly demonstrated using a DPPC/DPPE liposome model in the presence or absence of the NKA-selective inhibitor ouabain...
March 22, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28342833/a-high-density-cho-s-transient-transfection-system-comparison-of-expicho-and-expi293
#8
Nina K Jain, Susan Barkowski-Clark, Richard Altman, Krista Johnson, Fang Sun, Jonathan Zmuda, Chao Yan Liu, Adriana Kita, Ryan Schulz, Alyssa Neill, Robert Ballinger, Rekha Patel, Jian Liu, Alinafe Mpanda, Brian Huta, Henry Chiou, Walter Voegtli, Tadas Panavas
Chinese Hamster Ovary (CHO) cells are the principal mammalian host used for stable cell line generation and biotherapeutic protein production. Until recently, production of milligrams to grams of protein in CHO transient systems was challenging. As such, Human Embryonic Kidney (HEK293) cells are the most common mammalian cell type used for transient transfection. The post-translational modifications (PTMs) of a protein are dictated in part by the cell line used for expression, and changes in PTMs have been shown to affect both the activity and biophysical properties of proteins...
March 22, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28342806/molecular-regulation-of-mitochondrial-dynamics-in-cardiac-disease
#9
REVIEW
Jinliang Nan, Wei Zhu, M S Rahman, Mingfei Liu, Dan Li, Shengan Su, Na Zhang, Xinyang Hu, Hong Yu, Mahesh P Gupta, Jian''an Wang
Mitochondrial homeostasis is critical for keeping functional heart in response to metabolic or environmental stresses. Mitochondrial fission and fusion (mitochondrial dynamics) play essential roles in maintaining mitochondrial homeostasis, defects in mitochondrial dynamics lead to cardiac diseases such as ischemia-reperfusion injury (IRI), heart failure and diabetic cardiomyopathy. Mitochondrial dynamics is determined by mitochondrial fission and fusion proteins, including OPA1, mitofusins and Drp1. These proteins are tightly regulated by a series of signaling pathways through different aspects such as transcription, post translation modifications (PTMs) and proteasome-dependent protein degradation...
March 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28342553/myelin-changes-in-alexander-disease
#10
U Gómez-Pinedo, M Duran-Moreno, S Sirerol-Piquer, J Matias-Guiu
INTRODUCTION: Alexander disease (AxD) is a type of leukodystrophy. Its pathological basis, along with myelin loss, is the appearance of Rosenthal bodies, which are cytoplasmic inclusions in astrocytes. Mutations in the gene coding for GFAP have been identified as a genetic basis for AxD. However, the mechanism by which these variants produce the disease is not understood. DEVELOPMENT: The most widespread hypothesis is that AxD develops when a gain of function mutation causes an increase in GFAP...
March 22, 2017: Neurología: Publicación Oficial de la Sociedad Española de Neurología
https://www.readbyqxmd.com/read/28342303/cell-adaptation-upon-stress-the-emerging-role-of-membrane-less-compartments
#11
REVIEW
Catherine Rabouille, Simon Alberti
Cells under stress transition from a growth to a quiescent state. The conventional thinking is that this is achieved through transcriptional programs, translational regulation, protein degradation, and post-translational modifications. However, there is an increasing realization that stress adaptation also goes along with dramatic changes in the architecture and organization of cells. In particular, it seems to involve the formation of membrane-less compartments and macromolecular assemblies. We propose that cells make widespread use of this ability to change macromolecular organization to adapt to stress conditions and protect themselves...
March 22, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28342286/switching-aurora-a-kinase-on-and-off-at-an-allosteric-site
#12
REVIEW
Richard Bayliss, Selena G Burgess, Patrick J McIntyre
Protein kinases are central players in the regulation of cell cycle and signalling pathways. Their catalytic activities are strictly regulated through post-translational modifications and protein-protein interactions that control switching between inactive and active states. These states have been studied extensively using protein crystallography, although the dynamic nature of protein kinases makes it difficult to capture all relevant states. Here we describe two recent structures of Aurora-A kinase that trap its active and inactive states...
March 25, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28341852/profiling-of-long-non-coding-rnas-identifies-linc00958-and-linc01296-as-candidate-oncogenes-in-bladder-cancer
#13
Anna Katharina Seitz, Lise Lotte Christensen, Emil Christensen, Kasper Faarkrog, Marie Stampe Ostenfeld, Jakob Hedegaard, Iver Nordentoft, Morten Muhlig Nielsen, Johan Palmfeldt, Michelle Thomson, Michael Theis Solgaard Jensen, Roman Nawroth, Tobias Maurer, Torben Falck Ørntoft, Jørgen Bjerggaard Jensen, Christian Kroun Damgaard, Lars Dyrskjøt
Aberrant expression of long non-coding RNAs (lncRNAs) has been regarded as a critical component in bladder cancer (BC) and lncRNAs have been associated with BC development and progression although their overall expression and functional significance is still unclear. The aim of our study was to identify novel lncRNAs with a functional role in BC carcinogenesis. RNA-sequencing was used to identify aberrantly expressed lncRNAs in 8 normal and 72 BC samples. We identified 89 lncRNAs that were significantly dys-regulated in BC...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28341809/structural-basis-of-molecular-recognition-of-helical-histone-h3-tail-by-phd-finger-domains
#14
Alessio Bortoluzzi, Anastasia Amato, Xavier Lucas, Manuel Blank, Alessio Ciulli
The plant homeodomain (PHD) fingers are amongst the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation, however less is known about the recognition of secondary structure features within histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A (BAZ2A, also known as TIP5) in complex with unmodified N-terminal histone H3 tail...
March 24, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28341808/protein-coalation-a-redox-regulated-protein-modification-by-coenzyme-ain-mammalian-cells
#15
Yugo Tsuchiya, Sew Peak-Chew, Clare Newell, Sheritta Miller-Aidoo, Sriyash Mangal, Alexander Zhyvoloup, Jovana Baković, Oksana Malanchuk, Gonçalo Pereira, Vassilios Kotiadis, Gyorgy Szabadkai, Michael Duchen, Mark Campbell, Sergio Rodriguez Cuenca, Antonio Vidal-Puig, Andrew James, Michael P Murphy, Valeriy Filonenko, Mark Skehel, Ivan Gout
Coenzyme A (CoA) is an obligatory cofactor in all branches of life. CoA and its derivatives are involved in major metabolic pathways, allosteric interactions and the regulation of gene expression. Abnormal biosynthesis and homeostasis of CoA and its derivatives have been associated with various human pathologies, including cancer, diabetes and neurodegeneration. Using an anti-CoA monoclonal antibody and mass spectrometry we identified a wide range of cellular proteins which are modified by covalent attachment of CoA to cysteine thiols (CoAlation)...
March 24, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28341601/advances-in-maldi-imaging-mass-spectrometry-of-proteins-in-cardiac-tissue-including-the-heart-valve
#16
REVIEW
Peggi M Angel, H Scott Baldwin, Danielle Gottlieb, Yan Ru Su, John E Mayer, David Bichell, Richard R Drake
Significant progress has been made for tissue imaging of proteins using matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS). These advancements now facilitate mapping of a wide range of proteins, peptides, and post-translational modifications in a wide variety of tissues; however, the use of MALDI IMS to detect proteins from cardiac tissue is limited. This review discusses the most recent advances in protein imaging and demonstrates application to cardiac tissue, including the heart valve...
March 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28341406/sweet-new-roles-for-protein-glycosylation-in-prokaryotes
#17
REVIEW
Jerry Eichler, Michael Koomey
Long-held to be a post-translational modification unique to Eukarya, it is now clear that both Bacteria and Archaea also perform protein glycosylation, namely the covalent attachment of mono- to polysaccharides to specific protein targets. At the same time, many of the roles assigned to this protein-processing event in eukaryotes, such as guiding protein folding/quality control, intracellular trafficking, dictating cellular recognition events and others, do not apply or are even irrelevant to prokaryotes. As such, protein glycosylation must serve novel functions in Bacteria and Archaea...
March 21, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28340958/metabolism-and-acetylation-in-innate-immune-cell-function-and-fate
#18
REVIEW
Alanna M Cameron, Simon J Lawless, Edward J Pearce
Innate immunity is the first line of defense against invading pathogens. Changes in both metabolism and chromatin accessibility contribute to the shaping of these innate immune responses, and we are beginning to appreciate that cross-talk between these two systems plays an important role in determining innate immune cell differentiation and function. In this review we focus on acetylation, a post-translational modification important for both regulating chromatin accessibility by modulating histone function, and for functional regulation of non-histone proteins, which has many links to both immune signaling and metabolism...
October 2016: Seminars in Immunology
https://www.readbyqxmd.com/read/28340407/transmission-of-persistent-ionizing-radiation-induced-foci-through-cell-division-in-human-primary-cells
#19
Aurelie Vaurijoux, Pascale Voisin, Amelie Freneau, Joan Francesc Barquinero, Gaetan Gruel
Unrepaired DNA double-strand breaks (DSBs) induced by ionizing radiation are associated with lethal effects and genomic instability. After the initial breaks and chromatin destabilization, a set of post-translational modifications of histones occurs, including phosphorylation of serine 139 of histone H2AX (γH2AX), which leads to the formation of ionizing radiation-induced foci (IRIF). DSB repair results in the disappearance of most IRIF within hours after exposure, although some remain 24h after irradiation...
March 10, 2017: Mutation Research
https://www.readbyqxmd.com/read/28339907/o-linked-%C3%AE-n-acetylglucosamine-modification-of-proteins-is-essential-for-foot-process-maturation-and-survival-in-podocytes
#20
Shinya Ono, Shinji Kume, Mako Yasuda-Yamahara, Kosuke Yamahara, Naoko Takeda, Masami Chin-Kanasaki, Hisazumi Araki, Osamu Sekine, Hideki Yokoi, Masashi Mukoyama, Takashi Uzu, Shin-Ichi Araki, Hiroshi Maegawa
Background.: O-linked β- N -acetylglucosamine modification O-GlcNAcylation) is a post-translational modification of intracellular proteins, serving as a nutrient sensor. Growing evidence has demonstrated its physiological and pathological importance in various mammalian tissues. This study examined the physiological role of O-GlcNAcylation in podocyte function and development. Methods.: O-GlcNAc transferase (Ogt) is a critical enzyme for O-GlcNAcylation and resides on the X chromosome...
February 27, 2017: Nephrology, Dialysis, Transplantation
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