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https://www.readbyqxmd.com/read/28431276/enzymatic-activity-gene-expression-and-posttranslational-modifications-of-photosynthetic-and-non-photosynthetic-phosphoenolpyruvate-carboxylase-in-ammonium-stressed-sorghum-plants
#1
Cirenia Arias-Baldrich, Clara de la Osa, Nadja Bosch, Isabel Ruiz-Ballesta, José A Monreal, Sofía García-Mauriño
Sorghum plants grown with 5mM (NH4)2SO4 showed symptoms of stress, such as reduced growth and photosynthesis, leaf chlorosis, and reddish roots. Phosphoenolpyruvate carboxylase (PEPC) activity, by supplying carbon skeletons for ammonium assimilation, plays a pivotal role in tolerance to ammonium stress. This work investigated the effect of ammonium nutrition on PPC and PPCK gene expression, on PEPC activity, and on post-translational modifications (PTMs) of PEPC in leaves and roots of sorghum plants. Ammonium increased PEPC kinase (PEPCk) activity and the phosphorylation state of PEPC in leaves, both in light and in the dark, due to increased PPCK1 expression in leaves...
March 31, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28426469/prophylactic-radiotherapy-for-procedure-tract-metastases-in-mesothelioma-a-review
#2
David T Arnold, Amelia O Clive
PURPOSE OF REVIEW: Malignant pleural mesothelioma is an aggressive malignancy with a very poor prognosis. The majority of patients require pleural procedures for diagnostic or fluid management purposes. Damage to the pleura during these procedures can lead to procedure tract metastases (PTMs), with increasing risk from larger interventions. Prophylactic radiotherapy to these sites is a controversial topic with conflicting results from trial data. In this review, we summarize the recent evidence...
April 19, 2017: Current Opinion in Pulmonary Medicine
https://www.readbyqxmd.com/read/28426288/post-translational-modifications-of-rab-gtpases
#3
Swapnil Rohidas Shinde, Subbareddy Maddika
Rab GTPases, the highly conserved members of Ras GTPase superfamily are central players in the vesicular trafficking. They are critically involved in intracellular trafficking pathway, beginning from formation of vesicles on donor membranes, defining trafficking specificity to facilitating vesicle docking on target membranes. Given the dynamic roles of Rabs during different stages of vesicular trafficking, mechanisms for their spatial and temporal regulation are crucial for normal cellular function. Regulation of Rab GTPase activity, localization and function has always been focused in and around the association of GDP dissociation inhibitor (GDI), Guanine nucleotide Exchange Factor (GEFs) and GTPase accelerating protein (GAP) to Rabs...
February 28, 2017: Small GTPases
https://www.readbyqxmd.com/read/28425971/%C3%AF-%C3%A2-cells-feature-de-ubiquitination-of-slc-transporters-and-increased-levels-and-fluxes-of-amino-acids
#4
André Bordinassi Medina, Marcin Banaszczak, Yang Ni, Ina Aretz, David Meierhofer
Solute carrier (SLC) transporters are a diverse group of membrane transporter proteins that regulate the cellular flux and distribution of endogenous and xenobiotic compounds. Post-translational modifications (PTMs), such as ubiquitination, have recently emerged as one of the major regulatory mechanisms in protein function and localization. Previously, we showed that SLC amino acid transporters were on average 6-fold de-ubiquitinated and increased amino acid levels were detected in ρ⁰ cells (lacking mitochondrial DNA, mtDNA) compared to parental cells...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28412930/large-scale-analysis-of-post-translational-modifications-in-e-coli-under-glucose-limiting-conditions
#5
Colin W Brown, Viswanadham Sridhara, Daniel R Boutz, Maria D Person, Edward M Marcotte, Jeffrey E Barrick, Claus O Wilke
BACKGROUND: Post-translational modification (PTM) of proteins is central to many cellular processes across all domains of life, but despite decades of study and a wealth of genomic and proteomic data the biological function of many PTMs remains unknown. This is especially true for prokaryotic PTM systems, many of which have only recently been recognized and studied in depth. It is increasingly apparent that a deep sampling of abundance across a wide range of environmental stresses, growth conditions, and PTM types, rather than simply cataloging targets for a handful of modifications, is critical to understanding the complex pathways that govern PTM deposition and downstream effects...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28412815/high-throughput-analysis-of-intact-human-proteins-using-uvpd-and-hcd-on-an-orbitrap-mass-spectrometer
#6
Timothy P Cleland, Caroline J DeHart, Ryan T Fellers, Alexandra J VanNispen, Joseph B Greer, Richard D LeDuc, William Ryan Parker, Paul M Thomas, Neil L Kelleher, Jennifer S Brodbelt
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernable by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale...
April 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28408866/post-translational-modifications-and-protein-quality-control-in-motor-neuron-and-polyglutamine-diseases
#7
REVIEW
Fabio Sambataro, Maria Pennuto
Neurodegenerative diseases, including motor neuron and polyglutamine (polyQ) diseases, are a broad class of neurological disorders. These diseases are characterized by neuronal dysfunction and death, and by the accumulation of toxic aggregation-prone proteins in the forms of inclusions and micro-aggregates. Protein quality control is a cellular mechanism to reduce the burden of accumulation of misfolded proteins, a function that results from the coordinated actions of chaperones and degradation systems, such as the ubiquitin-proteasome system (UPS) and autophagy-lysosomal degradation system...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28408483/o-glcnac-cycling-and-the-regulation-of-nucleocytoplasmic-dynamics
#8
REVIEW
Moriah Eustice, Michelle R Bond, John A Hanover
The dynamic carbohydrate post-translational modification (PTM) O-linked β-N-acetyl glucosamine (O-GlcNAc) is found on thousands of proteins throughout the nucleus and cytoplasm, and rivals phosphorylation in terms of the number of substrates and pathways influenced. O-GlcNAc is highly conserved and essential in most organisms, with disruption of O-GlcNAc cycling linked to diseases ranging from cancer to neurodegeneration. Nuclear pore proteins were the first identified O-GlcNAc-modified substrates, generating intense and ongoing interest in understanding the role of O-GlcNAc cycling in nuclear pore complex structure and function...
April 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28406609/top-down-proteomics-of-large-proteins-up-to-223-kda-enabled-by-serial-size-exclusion-chromatography-strategy
#9
Wenxuan Cai, Trisha Tucholski, Bifan Chen, Andrew J Alpert, Sean McIlwain, Takushi Kohmoto, Song Jin, Ying Ge
Mass spectrometry (MS)-based top-down proteomics is a powerful method for the comprehensive analysis of proteoforms that arise from genetic variations and post-translational modifications (PTMs). However, top-down MS analysis of high molecular weight (MW) proteins remains challenging mainly due to the exponential decay of signal-to-noise ratio with increasing MW. Size exclusion chromatography (SEC) is a favored method for size-based separation of biomacromolecules, but typically suffers from low resolution...
April 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28406606/characterization-of-complete-histone-tail-proteoforms-using-differential-ion-mobility-spectrometry
#10
Pavel Vyacheslavovich Shliaha, Matthew A Baird, Mogens M Nielsen, Vladimir Gorshkov, Andrew P Bowman, Julia L Kaszycki, Ole Nørregaard Jensen, Alexandre A Shvartsburg
Histone proteins are subject to dynamic post-translational modifications (PTMs) that cooperatively modulate the chromatin structure and function. Nearly all functional PTMs are found on the N-terminal histone domains (tails) of ~50 residues protruding from the nucleosome core. Using high-definition differential ion mobility spectrometry (FAIMS) with electron transfer dissociation, we demonstrate rapid baseline gas-phase separation and identification of tails involving monomethylation, trimethyla-tion, acetylation, or phosphorylation in biologically relevant positions...
April 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28395773/improving-data-quality-and-preserving-hcd-generated-reporter-ions-with-ethcd-for-isobaric-tag-based-quantitative-proteomics-and-proteome-wide-ptm-studies
#11
Qing Yu, Xudong Shi, Yu Feng, K Craig Kent, Lingjun Li
Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states...
May 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28389918/quantitative-analysis-of-the-cysteine-redoxome-by-iodoacetyl-tandem-mass-tags
#12
Shakir Shakir, Joelle Vinh, Giovanni Chiappetta
The redox conditions that reign inside a cell have a determining effect on a number of biological processes. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are key redox players and have been linked to a number of pathologies. They have also been shown to play an important regulating role in cell signaling events. On the proteome level, thiol groups of cysteinyl side chains constitute the major targets of ROS and RNS. A number of analytical techniques based on mass spectrometry have been developed to characterize the cysteine redoxome, often facing a number of technical challenges, mostly related to the lability, heterogeneity, and low abundance of the oxidized forms...
April 7, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28381578/mutagenesis-of-dengue-virus-protein-ns2a-revealed-a-novel-domain-responsible-for-virus-induced-cytopathic-effect-and-interactions-between-ns2a-and-ns2b-transmembrane-segments
#13
Ren-Huang Wu, Ming-Han Tsai, Kuen-Nan Tsai, Jia Ni Tian, Jian-Sung Wu, Su-Ying Wu, Jyh-Haur Chern, Chun-Hong Chen, Andrew Yueh
The NS2A protein of Dengue virus (DENV) has eight predicted transmembrane segments (pTMS1-8) and participates in RNA replication, virion assembly, and host antiviral response. However, the roles of specific amino acid residues within the pTMS regions of NS2A during the viral life cycle are not clear. Here, we explored the function of DENV NS2A by introducing a series of alanine substitutions into the N-terminal half (pTMS1-4) of the protein in the context of a DENV infectious clone or subgenomic replicon. Six NS2A mutants (NM5, 7, 9, and 17-19) around pTMS1-2 displayed a novel phenotype showing a >1000-fold reduction in virus yield, an absence of plaque formation despite wild-type-like replicon activity, and infectious virus-like particle yields...
April 5, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28377601/quantitative-chromatin-proteomics-reveals-a-dynamic-histone-post-translational-modification-landscape-that-defines-asexual-and-sexual-plasmodium-falciparum-parasites
#14
Nanika Coetzee, Simone Sidoli, Riëtte van Biljon, Heather Painter, Manuel Llinás, Benjamin A Garcia, Lyn-Marie Birkholtz
Gene expression in Plasmodia integrates post-transcriptional regulation with epigenetic marking of active genomic regions through histone post-translational modifications (PTMs). To generate insights into the importance of histone PTMs to the entire asexual and sexual developmental cycles of the parasite, we used complementary and comparative quantitative chromatin proteomics to identify and functionally characterise histone PTMs in 8 distinct life cycle stages of P. falciparum parasites. ~500 individual histone PTMs were identified of which 106 could be stringently validated...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28373551/identification-of-specific-posttranslational-o-mycoloylations-mediating-protein-targeting-to-the-mycomembrane
#15
Clément Carel, Julien Marcoux, Valérie Réat, Julien Parra, Guillaume Latgé, Françoise Laval, Pascal Demange, Odile Burlet-Schiltz, Alain Milon, Mamadou Daffé, Maryelle G Tropis, Marie A M Renault
The outer membranes (OMs) of members of the Corynebacteriales bacterial order, also called mycomembranes, harbor mycolic acids and unusual outer membrane proteins (OMPs), including those with α-helical structure. The signals that allow precursors of such proteins to be targeted to the mycomembrane remain uncharacterized. We report here the molecular features responsible for OMP targeting to the mycomembrane of Corynebacterium glutamicum, a nonpathogenic member of the Corynebacteriales order. To better understand the mechanisms by which OMP precursors were sorted in C...
April 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28372234/deamidation-post-translational-modification-in-naturally-generated-peptides-in-spanish-dry-cured-ham
#16
Manuel Cañete, Leticia Mora, Fidel Toldrá
A large number of peptides are generated during the processing of dry-cured ham that can be affected by post-translational modifications (PTM). One of the most studied PTMs is the oxidation of susceptible residues but other modifications such as deamidation have been scarcely reported in the literature. This work has been focused on the impact of deamidation in those peptides generated in 12-months dry-cured hams. The results obtained in Biceps femoris and Semimembranosus muscles showed that 52% and 48% of the identified peptides, respectively, were affected by PTMs, with a total of 277 and 282 sequences showing deamidation in both muscles, respectively...
August 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28371718/comparability-study-of-rituximab-originator-and-follow-on-biopharmaceutical
#17
Othman Montacir, Houda Montacir, Murat Eravci, Andreas Springer, Stephan Hinderlich, Amirhossein Saadati, Maria Kristina Parr
Immunglobolin G (IgG)-based biopharmaceuticals are emerging on the pharmaceuticals market due to their high target selectivity in different diseases. In parallel, a growing interest by other companies to produce similar or highly similar follow-on biologics exits, once the patent of blockbuster biotherapeutics is about to expire. In correlation to their complex structure, an analytical challenge is facing the approval of these biosimilars. Health authorities (e.g. FDA and EMA) have issued several guidelines to define critical quality attributes during manufacturing process changes...
March 19, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28366003/complete-characterization-of-cardiac-myosin-heavy-chain-223-kda-enabled-by-size-exclusion-chromatography-and-middle-down-mass-spectrometry
#18
Yutong Jin, Liming Wei, Wenxuan Cai, Ziqing Lin, Zhijie Wu, Ying Peng, Takushi Kohmoto, Richard L Moss, Ying Ge
Myosin heavy chain (MHC), the major component of myosin motor molecule, plays an essential role in force production during muscle contraction. However, a comprehensive analysis of MHC proteoforms arising from sequence variations and post-translational modifications (PTMs) remains challenging due to the difficulties in purifying MHC (~223 kDa) and achieving complete sequence coverage. Herein, we have established a strategy to effectively purify and comprehensively characterize MHC from heart tissue by combining size-exclusion chromatography (SEC) and middle-down mass spectrometry (MS)...
April 1, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28360947/a-novel-method-for-isolation-of-histones-from-serum-and-its-implications-in-therapeutics-and-prognosis-of-solid-tumours
#19
Divya Reddy, Bharat Khade, Riddhi Pandya, Sanjay Gupta
BACKGROUND: Dysregulation in post-translational modifications of histones and their modifiers are now well-recognized as a hallmark of cancer and can be used as biomarkers and potential therapeutic targets for disease progression and prognosis. In most solid tumours, a biopsy is challenging, costly, painful or potentially risky for the patient. Therefore, non-invasive methods like 'liquid biopsy' for analysis of histone modifications and their modifiers if possible will be helpful in the better clinical management of cancer patients...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28358161/post-translational-modifications-involved-in-the-biosynthesis-of-thiopeptide-antibiotics
#20
REVIEW
Qingfei Zheng, Hui Fang, Wen Liu
Thiopeptide antibiotics are a class of typical ribosomally synthesized and post-translationally modified peptides (RiPPs) with complex chemical structures that are difficult to construct via chemical synthesis. To date, more than 100 thiopeptides have been discovered, and most of these compounds exhibit remarkable biological activities, such as antibacterial, antitumor and immunosuppressive activities. Therefore, studies of the biosynthesis of thiopeptides can contribute to the development of new drug leads and facilitate the understanding of the complex post-translational modifications (PTMs) of peptides and/or proteins...
April 18, 2017: Organic & Biomolecular Chemistry
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