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Inderjeet Kaur, Mohammad Zeeshan, Ekta Saini, Abhinav Kaushik, Asif Mohmmed, Dinesh Gupta, Pawan Malhotra
Post-transcriptional and post-translational modifications play a major role in Plasmodium life cycle regulation. Lysine methylation of histone proteins is well documented in several organisms, however in recent years lysine methylation of proteins outside histone code is emerging out as an important post-translational modification (PTM). In the present study we have performed global analysis of lysine methylation of proteins in asexual blood stages of Plasmodium falciparum development. We immunoprecipitated stage specific Plasmodium lysates using anti-methyl lysine specific antibodies that immunostained the asexual blood stage parasites...
October 20, 2016: Scientific Reports
Simona Citro, Susanna Chiocca
Attachment of ubiquitin or ubiquitin-like (Ubl) modifiers, such as the small ubiquitin-related modifier SUMO, is a posttranslational modification (PTM) that reversibly regulates the function and the stability of target proteins. The SUMO paralogs SUMO1 and SUMO2/3, although sharing a common conjugation pathway, seem to play different roles in the cell. Many regulatory mechanisms, which contribute to SUMO-paralog-specific modification, have emerged. We have recently found that cell environment affects SUMO-paralog-specific sumoylation of HDAC1, whose conjugation to SUMO1 and not to SUMO2 facilitates its protein turnover...
2017: Methods in Molecular Biology
Eva Liñeiro, Cristina Chiva, Jesús M Cantoral, Eduard Sabido, Francisco Javier Fernández-Acero
Phosphorylation is one of the main post-translational modification (PTM) involved in signaling network in the ascomycete Botrytis cinerea, one of the most relevant phytopathogenic fungus. The data presented in this article provided a differential mass spectrometry-based analysis of the phosphoproteome of B. cinerea under two different phenotypical conditions induced by the use of two different elicitors: glucose and deproteinized Tomate Cell Walls (TCW). A total 1138 and 733 phosphoproteins were identified for glucose and TCW culture conditions respectively...
June 2016: Data in Brief
Rafeeque R Alyethodi, Rajib Deb, Rani Alex, Sushil Kumar, Umesh Singh, Shrikant Tyagi, D K Mandal, T V Raja, A K Das, Sheetal Sharma, Gyanendra S Sengar, Rani Singh, B Prakash
Cryopreservation is one of the most important aspects of frozen semen technology and livestock breeding. Uses of candidate molecular markers in selection strategies for male fertility are well recognized. The present investigation targeted two microsatellite markers (BM1500 and UMN 2008) for association with semen quality variables and freezing capacity in Frieswal (HF×Sahiwal) crossbred bulls of Indian origin. Of the different alleles at the polymorphic locus BM1500, the 136bp allele was associated with greater (P<0...
October 11, 2016: Animal Reproduction Science
Fengchao Yu, Ning Li, Weichuan Yu
In computational proteomics, identification of peptides with an unlimited number of post-translational modification (PTM) types is a challenging task. The computational cost associated with database search increases exponentially with respect to the number of modified amino acids and linearly with respect to the number of potential PTM types at each amino acid. The problem becomes intractable very quickly if we want to enumerate all possible PTM patterns. To address this issue, one group of methods named restricted tools (including Mascot, Comet, and MS-GF+) only allow a small number of PTM types in database search process...
October 17, 2016: Journal of Proteome Research
Serena Marcelli, Elena Ficulle, Filomena Iannuzzi, Enikö Kövari, Robert Nisticò, Marco Feligioni
Synaptic dysfunction has been recognized as an early feature occurring at the onset of Alzheimer's disease (AD). Compromised neurotransmission leads over time to synaptic loss and these events correlate with the cognitive decline that progressively affects AD patients.Protein SUMOylation (Small Ubiquitin-like MOdifier) is a post-translational modification (PTM) involved in several cellular processes including synaptic transmission.We here demonstrate that cortical synaptosomes prepared from Tg2576 mice of 6 months of age show an increased SUMO-1ylation, which returns back to normal levels at 20 months although synaptic SUMOylation, at this age, resulted more sensible to KCl stimulus...
October 13, 2016: Molecular Neurobiology
R R da Cunha Filho, H L de Almeida, J D Basei, R H Camina, L A S de Castro
Pretibial myxedema (PTM) results from the accumulation of hyaluronic acid in the dermis and subcutis and is commonly associated with Graves' disease (GD). It occurs in up to 5% of patients with GD and in 13% of patients with GD and ophthalmopathy. PTM occasionally occurs in thyrotoxicosis but is much less frequently in patients with Hashimoto thyroiditis, primary hypothyroidism and euthyroidism. This article is protected by copyright. All rights reserved.
October 12, 2016: Journal of the European Academy of Dermatology and Venereology: JEADV
Jacqueline R Rivas, Sara J Ireland, Rati Chkheidze, William H Rounds, Joseph Lim, Jordan Johnson, Denise M O Ramirez, Ann J Ligocki, Ding Chen, Alyssa A Guzman, Mark Woodhall, Patrick C Wilson, Eric Meffre, Charles White, Benjamin M Greenberg, Patrick Waters, Lindsay G Cowell, Ann M Stowe, Nancy L Monson
Plasmablasts are a highly differentiated, antibody secreting B cell subset whose prevalence correlates with disease activity in Multiple Sclerosis (MS). For most patients experiencing partial transverse myelitis (PTM), plasmablasts are elevated in the blood at the first clinical presentation of disease (known as a clinically isolated syndrome or CIS). In this study we found that many of these peripheral plasmablasts are autoreactive and recognize primarily gray matter targets in brain tissue. These plasmablasts express antibodies that over-utilize immunoglobulin heavy chain V-region subgroup 4 (VH4) genes, and the highly mutated VH4+ plasmablast antibodies recognize intracellular antigens of neurons and astrocytes...
October 11, 2016: Acta Neuropathologica
Bart O Roep, Maria Jl Kracht, Menno van Lummel, Arnaud Zaldumbide
Type 1 diabetes (T1D) is an autoimmune disease characterized by the selective destruction of the insulin-producing beta cells. Beta cell dysfunction caused by an inflammatory microenvironment is believed to trigger the peripheral activation of CD4 and CD8 autoreactive T cells. This review will compile post-transcriptional and post-translational modifications (PTM) involved in the generation of beta cell neoantigens and proposes a reconstruction of the sequence of events connecting environmental changes and autoimmunity...
October 7, 2016: Current Opinion in Immunology
Alexander V Rudnev, Carlos Franco, Núria Crivillers, Gonca Seber, Andrea Droghetti, Ivan Rungger, Ilya V Pobelov, Jaume Veciana, Marta Mas-Torrent, Concepció Rovira
A redox-active persistent perchlorotriphenylmethyl (PTM) radical chemically linked to gold exhibits stable electrochemical activity in ionic liquids. Electrochemical tunnelling spectroscopy in this medium demonstrates that the PTM radical shows a highly effective redox-mediated current enhancement, demonstrating its applicability as an active nanometer-scale electronic component.
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
L Yang, X Li, M F Liu, P L Li, Z B Yan, M Zeng, M H Qin, X S Gao, J-M Liu
The magnetically induced electric polarization behaviors in multiferroic TmMn2O5 in response to varying temperature and magnetic field are carefully investigated by means of a series of characterizations including the high precision pyroelectric current technique. Here polycrystalline rather than single crystal samples are used for avoiding the strong electrically self-polarized effect in single crystals, and various parallel experiments on excluding the thermally excited current contributions are performed...
October 7, 2016: Scientific Reports
Barry M Zee, Amy B Dibona, Artyom A Alekseyenko, Christopher A French, Mitzi I Kuroda
Defects in chromatin proteins frequently manifest in diseases. A striking case of a chromatin-centric disease is NUT-midline carcinoma (NMC), which is characterized by expression of NUT as a fusion partner most frequently with BRD4. ChIP-sequencing studies from NMC patients revealed that BRD4-NUT (B4N) covers large genomic regions and elevates transcription within these domains. To investigate how B4N modulates chromatin, we performed affinity purification of B4N when ectopically expressed in 293-TREx cells and quantified the associated histone posttranslational modifications (PTM) using proteomics...
2016: PloS One
Matthew Torres, Henry Dewhurst, Niveda Sundararaman
Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function &- a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) &- a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al...
October 3, 2016: Molecular & Cellular Proteomics: MCP
Christina M Woo, Alejandra Felix, Lichao Zhang, Joshua E Elias, Carolyn R Bertozzi
Protein glycosylation is a post-translational modification (PTM) responsible for many aspects of proteomic diversity and biological regulation. Assignment of intact glycan structures to specific protein attachment sites is a critical step towards elucidating the function encoded in the glycome. Previously, we developed isotope-targeted glycoproteomics (IsoTaG) as a mass-independent mass spectrometry method to characterize azide-labeled intact glycopeptides from complex proteomes. Here, we extend the IsoTaG approach with the use of alkynyl sugars as metabolic labels and employ new probes in analysis of the sialylated glycoproteome from PC-3 cells...
September 30, 2016: Analytical and Bioanalytical Chemistry
Sheo B Singh, Ling Kang, Andrea R Nawrocki, Dan Zhou, Margaret Wu, Stephen Previs, Corey Miller, Haiying Liu, Catherine D G Hines, Maria Madeira, Jin Cao, Kithsiri Herath, Liangsu Wang, David E Kelley, Cai Li, Hong-Ping Guan
OBJECTIVES: Platensimycin (PTM) is a natural antibiotic produced by Streptomyces platensis that selectively inhibits bacterial and mammalian fatty acid synthase (FAS) without affecting synthesis of other lipids. Recently, we reported that oral administration of PTM in mouse models (db/db and db/+) with high de novo lipogenesis (DNL) tone inhibited DNL and enhanced glucose oxidation, which in turn led to net reduction of liver triglycerides (TG), reduced ambient glucose, and improved insulin sensitivity...
2016: PloS One
Nadav Brandes, Dan Ofer, Michal Linial
Determining residue-level protein properties, such as sites of post-translational modifications (PTMs), is vital to understanding protein function. Experimental methods are costly and time-consuming, while traditional rule-based computational methods fail to annotate sites lacking substantial similarity. Machine Learning (ML) methods are becoming fundamental in annotating unknown proteins and their heterogeneous properties. We present ASAP (Amino-acid Sequence Annotation Prediction), a universal ML framework for predicting residue-level properties...
2016: Database: the Journal of Biological Databases and Curation
José M Rodríguez-Vargas, María I Rodríguez, Jara Majuelos-Melguizo, Ángel García-Diaz, Ariannys González-Flores, Abelardo López-Rivas, László Virág, Giuditta Illuzzi, Valerie Schreiber, Françoise Dantzer, F Javier Oliver
AMPK is a central energy sensor linking extracellular milieu fluctuations with the autophagic machinery. In the current study we uncover that Poly(ADP-ribosyl)ation (PARylation), a post-translational modification (PTM) of proteins, accounts for the spatial and temporal regulation of autophagy by modulating AMPK subcellular localisation and activation. More particularly, we show that the minority AMPK pool needs to be exported to the cytosol in a PARylation-dependent manner for optimal induction of autophagy, including ULK1 phosphorylation and mTORC1 inactivation...
September 30, 2016: Cell Death and Differentiation
Aida Serra, Xavier Gallart-Palau, Juan Wei, Siu Kwan Sze
Deamidation of glutamine (Gln) residues is a spontaneous or enzymatic process with significant implications in aging and human pathology. Although some methods are available to identify the γ/α-glutamyl products of deamidation, none of these methods allows the characterization of this post-translational modification (PTM) from complex biological samples by shotgun proteomics. Here we present LERLIC-MS/MS, a chromatographic strategy that uses a long (50 cm) anion-exchange capillary column operating in the electrostatic repulsion-hydrophilic interaction mode (ERLIC) and coupled directly to tandem mass spectrometry (MS/MS) for proteome analysis in a single injection...
October 13, 2016: Analytical Chemistry
Akhilesh Kumar, Michael D Birnbaum, Devang M Patel, William M Morgan, Jayanti Singh, Antoni Barrientos, Fangliang Zhang
Arginyltransferase 1 (Ate1) mediates protein arginylation, a poorly understood protein posttranslational modification (PTM) in eukaryotic cells. Previous evidence suggest a potential involvement of arginylation in stress response and this PTM was traditionally considered anti-apoptotic based on the studies of individual substrates. However, here we found that arginylation promotes cell death and/or growth arrest, depending on the nature and intensity of the stressing factor. Specifically, in yeast, mouse and human cells, deletion or downregulation of the ATE1 gene disrupts typical stress responses by bypassing growth arrest and suppressing cell death events in the presence of disease-related stressing factors, including oxidative, heat, and osmotic stresses, as well as the exposure to heavy metals or radiation...
2016: Cell Death & Disease
Daniel J DelloStritto, Pritam Sinharoy, Patrick J Connell, Joseph N Fahmy, Holly C Cappelli, Charles K Thodeti, Werner J Geldenhuys, Derek S Damron, Ian N Bratz
We demonstrated previously that TRPV1-dependent regulation of coronary blood flow (CBF) is disrupted in diabetes. Further, we have shown that endothelial TRPV1 is differentially regulated, ultimately leading to the inactivation of TRPV1, when exposed to a prolonged pathophysiological oxidative environment. This environment has been shown to increase lipid peroxidation byproducts including 4-Hydroxynonenal (4-HNE). 4-HNE is notorious for producing protein post-translation modification (PTM) via reactions with the amino acids: cysteine, histidine and lysine...
September 25, 2016: Free Radical Biology & Medicine
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