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Post translational modifications

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https://www.readbyqxmd.com/read/29792883/plasma-n-glycan-signatures-associate-with-features-of-inflammatory-bowel-diseases
#1
Florent Clerc, Mislav Novokmet, Viktoria Dotz, Karli R Reiding, Noortje de Haan, Guinevere S M Kammeijer, Hans Dalebout, Marco R Bladergroen, Frano Vukovic, Erdmann Rapp, Stephan R Targan, Gildardo Barron, Natalia Manetti, Anna Latiano, Dermot P B McGovern, Vito Annese, Gordan Lauc, Manfred Wuhrer
BACKGROUND & AIMS: Biomarkers are needed for early detection of Crohn's disease (CD) and ulcerative colitis (UC) or to predict patient outcomes. Glycosylation is a common and complex post-translational modification of proteins that affects their structure and activity. We compared plasma N-glycosylation profiles between patients with CD or UC and healthy individuals (controls). METHODS: We analyzed the total plasma N-glycomes of 2635 patients with inflammatory bowel diseases and 996 controls by mass spectrometry with a linkage-specific sialic acid derivatization technique...
May 21, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29792876/temperature-dependent-sex-determination-realized-by-hormonal-dynamics-with-enzymatic-reactions-sensitive-to-ambient-temperature
#2
Sachi Yamaguchi, Yoh Iwasa
Temperature-dependent sex determination (TSD) is adopted by many animal taxa, including reptiles and fishes. In some species, the eggs develop into females under a low hatching temperature, whereas they will develop into males under a high hatching temperature (called the FM-pattern). In other species, the eggs develop into males (or females) under a low (or high) hatching temperature (MF-pattern). Still, in other species, the eggs develop into females, males, or females, respectively, when under a low, intermediate, or high hatching temperature (FMF-pattern)...
May 21, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29792811/tandem-mass-spectrometry-of-peptide-ions-by-microwave-excited-hydrogen-and-water-plasmas
#3
Yuji Shimabukuro, Hidenori Takahashi, Shinichi Iwamoto, Koichi Tanaka, Motoi Wada
A thermal cracking cell that served as the atomic hydrogen source for hydrogen attachment/abstraction dissociation (HAD) analysis has an intrinsic problem to produce a beam of atoms reactive against heated tungsten capillary. A plasma excited by 2.45 GHz microwave power can deliver reactive species to a quadrupole ion trap confining analyte ions without excessive heating of the radical source components. The radical (H•) production performance of the developed source was evaluated by optical emission spectroscopy and H• attachment reaction to fullerene ions...
May 24, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29791853/p27-kip1-modulates-axonal-transport-by-regulating-%C3%AE-tubulin-acetyltransferase-1-stability
#4
Giovanni Morelli, Aviel Even, Ivan Gladwyn-Ng, Romain Le Bail, Michal Shilian, Juliette D Godin, Elise Peyre, Bassem A Hassan, Arnaud Besson, Jean-Michel Rigo, Miguel Weil, Bert Brône, Laurent Nguyen
The protein p27Kip1 plays roles that extend beyond cell-cycle regulation during cerebral cortex development, such as the regulation of neuronal migration and neurite branching via signaling pathways that converge on the actin and microtubule cytoskeletons. Microtubule-dependent transport is essential for the maturation of neurons and the establishment of neuronal connectivity though synapse formation and maintenance. Here, we show that p27Kip1 controls the transport of vesicles and organelles along the axon of mice cortical projection neurons in vitro...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791133/design-construction-and-validation-of-histone-binding-effectors-in-vitro-and-in-cells
#5
Stefan J Tekel, Cassandra M Barrett, Daniel A Vargas, Karmella A Haynes
Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior, and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers...
May 23, 2018: Biochemistry
https://www.readbyqxmd.com/read/29790907/application-of-network-smoothing-to-glycan-lc-ms-profiling
#6
Joshua Klein, Luis Carvalho, Joseph Zaia
Motivation: Glycosylation is one of the most heterogeneous and complex protein post-translational modifications. Liquid chromatography coupled mass spectrometry (LC-MS) is a common high throughput method for analyzing complex biological samples. Accurate study of glycans require high resolution mass spectrometry. Mass spectrometry data contains intricate sub-structures that encode mass and abundance, requiring several transformations before it can be used to identify biological molecules, requiring automated tools to analyze samples in a high throughput setting...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790754/epiprofile-2-0-a-computational-platform-for-processing-epi-proteomics-mass-spectrometry-data
#7
Zuo-Fei Yuan, Simone Sidoli, Dylan M Marchione, Johayra Simithy, Kevin A Janssen, Mary R Szurgot, Benjamin A Garcia
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here, we present EpiProfile 2.0, an extended version of our 2015 software (v1.0) for accurate quantification of histone peptides based on liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis...
May 23, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29790249/the-mechanisms-of-epigenetic-inheritance-how-diverse-are-they
#8
Oleg N Tikhodeyev
Although epigenetic inheritance (EI) is a rapidly growing field of modern biology, it still has no clear place in fundamental genetic concepts which are traditionally based on the hereditary role of DNA. Moreover, not all mechanisms of EI attract the same attention, with most studies focused on DNA methylation, histone modification, RNA interference and amyloid prionization, but relatively few considering other mechanisms such as stable inhibition of plastid translation. Herein, we discuss all known and some hypothetical mechanisms that can underlie the stable inheritance of phenotypically distinct hereditary factors that lack differences in DNA sequence...
May 22, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29790184/fat10-overexpression-disturbs-wisp1-protein-and-mrna-expression-to-promote-hepatocellular-carcinoma-progression
#9
Jinlong Yan, Jun Lei, Leifeng Chen, Huan Deng, Dingxiang Dong, Tao Jin, Xiuxia Liu, Rongfa Yuan, Yumin Qiu, Jin Ge, Xiaogang Peng, Jianghua Shao
Recently, studies on transcriptome-proteome relationships have revealed mRNA/protein expression discordance for certain genes and speculated that protein post-translational modification (PTM) may be involved. However, there is currently no evidence to support this hypothesis. Wnt-induced secreted protein-1 (WISP1) is the downstream target gene of β-catenin and plays an important role in tumorigenesis and progression, but the expression and role of WISP1 in different tumor types are controversial. Here, we first confirmed WISP1 protein expression was significantly downregulated in hepatocellular carcinoma (HCC) tissue, and could be an independent predictor of poor prognosis for patients with HCC...
May 23, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29790151/irreversible-modifications-of-receptor-tyrosine-kinases
#10
Matthew Kreitman, Ashish Noronha, Yosef Yarden
Each group of the 56 receptor tyrosine kinases (RTK) binds with one or more soluble growth factors and coordinates a vast array of cellular functions. These outcomes are tightly regulated by inducible post-translational events, such as tyrosine phosphorylation, ubiquitination, ectodomain shedding and regulated intramembrane proteolysis. Because of the delicate balance required for appropriate RTK function, cells may become pathogenic upon dysregulation of RTKs themselves or their post-translational covalent modifications...
May 22, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29788207/potentiating-hsp104-activity-via-phosphomimetic-mutations-in-the-middle-domain
#11
Amber Tariq, JiaBei Lin, Megan M Noll, Mariana P Torrente, Korrie L Mack, Oscar Hernandez Murillo, Meredith E Jackrel, James Shorter
Hsp104 is a hexameric AAA + ATPase and protein disaggregase found in yeast, which can be potentiated via mutations in its middle domain (MD) to counter toxic phase separation by TDP-43, FUS and α-synuclein connected to devastating neurodegenerative disorders. Subtle missense mutations in the Hsp104 MD can enhance activity, indicating that post-translational modification of specific MD residues might also potentiate Hsp104. Indeed, several serine and threonine residues throughout Hsp104 can be phosphorylated in vivo...
August 1, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29787816/o-glcnacylation-and-neuronal-energy-status-implications-for-alzheimer-s-disease
#12
REVIEW
Tiffany S Pinho, Diogo M Verde, Sónia C Correia, Susana M Cardoso, Paula I Moreira
Since the first clinical case reported more than 100 years ago, it has been a long and winding road to demystify the initial pathological events underling the onset of Alzheimer's disease (AD). Fortunately, advanced imaging techniques extended the knowledge regarding AD origin, being well accepted that a decline in brain glucose metabolism occurs during the prodromal phases of AD and is aggravated with the progression of the disease. In this sense, in the last decades, the post-translational modification O-linked β-N-acetylglucosaminylation (O-GlcNAcylation) has emerged as a potential causative link between hampered brain glucose metabolism and AD pathology...
May 19, 2018: Ageing Research Reviews
https://www.readbyqxmd.com/read/29787335/platelet-proteomics-from-discovery-to-diagnosis
#13
Christina Looße, Frauke Swieringa, Johan W M Heemskerk, Albert Sickmann, Christin Lorenz
Platelets are the smallest cells within the circulating blood with key roles in physiological haemostasis and pathological thrombosis regulated by the onset of activating/inhibiting processes via receptor responses and signalling cascades. Areas covered: Proteomics as well as genomic approaches have been fundamental in identifying and quantifying potential targets for future diagnostic strategies in the prevention of bleeding and thrombosis, and uncovering the complexity of platelet functions in health and disease...
May 22, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29786648/utilizing-optimized-tools-to-investigate-ptm-crosstalk-identifying-potential-ptm-crosstalk-of-acetylated-mitochondrial-proteins
#14
Henrick Horita, Andy Law, Kim Middleton
Post-translational modification (PTM) crosstalk is recognized as a major cell-regulatory mechanism, and studies of several proteins have validated the premise that PTMs work in concert. Previous work by our group investigated the potential PTM crosstalk on proteins in the EGFR-Ras-c-Fos axis by utilizing a comprehensive set of PTM reagents termed Signal-Seeker toolkits. In this study, these tools were used to investigate the potential PTM crosstalk that occurs in acetylated mitochondrial proteins in response to a mitochondrial stress-inducing agent hydrogen peroxide (H₂O₂)...
May 22, 2018: Proteomes
https://www.readbyqxmd.com/read/29786419/multifunctional-high-molecular-weight-post-translationally-modified-proteins-through-oxidative-cysteine-coupling-and-tyrosine-modification
#15
Brian M Seifried, James Cao, Bradley D Olsen
Glycoproteins and their mimics are challenging to produce via chemical or biological methods because of their long protein backbones and large number of polysaccharide side chains that form a densely grafted protein-polysaccharide brush architecture. Herein, we demonstrate a new approach to protein bioconjugate synthesis that can approach the molar mass and functionalization densities of natural glycoproteins such as mucins and aggrecans. In this method, a tyrosine-enriched protein sequence is engineered and synthesized in E...
May 22, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29784880/arginine-methylation-of-translocated-in-liposarcoma-tls-inhibits-its-binding-to-long-noncoding-rna-abrogating-tls-mediated-repression-of-cbp-p300-activity
#16
Wei Cui, Ryoma Yoneda, Naomi Ueda, Riki Kurokawa
Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A-binding protein P300 (p300) on the cyclin D1 (CCND1) gene. Although post-translational modifications of TLS, such as arginine methylation, are known to regulate TLS's nucleocytoplasmic shuttling and assembly in stress granules, its interactions with RNAs remain poorly characterized...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784649/small-molecular-inhibitors-targeting-protein-sumoylation-as-novel-anticancer-compounds
#17
Yanfang Yang, Zijing Xia, Xixi Wang, Xinyu Zhao, Zenghua Sheng, Yang Ye, Gu He, Liangxue Zhou, Hongxia Zhu, Ningzhi Xu, Shufang Liang
SUMOylation, one of post-translational modifications, is covalently modified on lysine residues of a target protein through an enzymatic cascade reaction similar to protein ubiquitination. Along with identification of many SUMOylated proteins, protein SUMOylation has been proven to regulate multiple biological activities including transcription, cell cycle, DNA repair and innate immunity. The dysregulation of protein SUMOylation and deSUMOylation modification is linked with carcinogenesis and tumor progression...
May 21, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29784645/harnessing-post-translational-modifications-for-next-generation-hiv-immunogens
#18
REVIEW
Joel D Allen, Rogier W Sanders, Katie J Doores, Max Crispin
The extensive post-translational modifications of the envelope spikes of the human immunodeficiency virus (HIV) present considerable challenges and opportunities for HIV vaccine design. These oligomeric glycoproteins typically have over 30 disulfide bonds and around a 100 N-linked glycosylation sites, and are functionally dependent on protease cleavage within the secretory system. The resulting mature structure adopts a compact fold with the vast majority of its surface obscured by a protective shield of glycans which can be targeted by broadly neutralizing antibodies (bnAbs)...
May 21, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29784395/development-a-hydrazide-functionalized-thermosensitive-polymer-based-homogeneous-system-for-highly-efficient-n-glycoprotein-glycopeptide-enrichment-from-human-plasma-exosome
#19
Haihong Bai, Yiting Pan, Lu Qi, Long Liu, Xinyuan Zhao, Hangyan Dong, Xiaoqiang Cheng, Weijie Qin, Xinghe Wang
As one of the most common post-translational modifications, protein N-glycosylation precipitates in many important biological processes and has closely correlations with the occurrence and progression of multiple diseases. Plasma exosomes secreted by cells contain various bioactive N-glycoproteins which may serve as potential biomarkers for early disease diagnosis and treatment. However, the protein N-glycosylation profile in human plasma exosome is largely unknown, due to the technical challenges in glycoprotein identification...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29783946/novel-flax-orbitide-derived-from-genetic-deletion
#20
Peta-Gaye Gillian Burnett, Lester Warren Young, Clara Marisa Olivia, Pramodkumar Dinkar Jadhav, Denis Paskal Okinyo-Owiti, Martin John Tarsisius Reaney
BACKGROUND: Flaxseed orbitides are homodetic plant cyclic peptides arising from ribosomal synthesis and post-translation modification (N to C cyclization), and lacking cysteine double bonds (Nat Prod Rep 30:108-160, 2013). Screening for orbitide composition was conducted on the flax core collection (FCC) grown at both Saskatoon, Saskatchewan and Morden, Manitoba over three growing seasons (2009-2011). Two flax (Linum usitatissimum L.) accessions 'Hollandia' (CN 98056) and 'Z 11637' (CN 98150) produce neither [1-9-NαC]-linusorb B2 (3) nor [1-9-NαC]-linusorb B3 (1)...
May 21, 2018: BMC Plant Biology
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