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https://www.readbyqxmd.com/read/28428430/collagen-beta-1-o-galactosyltransferase-1-glt25d1-is-required-for-the-secretion-of-high-molecular-weight-adiponectin-and-affects-lipid-accumulation
#1
Julie A Webster, Zhe Yang, Yu-Hee Kim, Dorothy Loo, Rasha M Mosa, Hongzhuo Li, Chen Chen
Secretion of high molecular weight (HMW) adiponectin is dependent on post-translational modification (PTM) of conserved lysines in the collagenous domain. This work aims to characterize the enzymes responsible for the PTM of conserved lysines which leads to HMW adiponectin secretion, and to define its significance in relation to obesity.  Collagen beta (1- O ) galactosyltransferase 1 (GLT25D1) was knocked down in HEK cells modified for the stable expression of adiponectin (Adipo-HEK cells) as well as in Simpson Golabi-Behmel-Syndrome (SGBS) adipocytes...
April 20, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28425870/ipreny-pseaac-identify-c-terminal-cysteine-prenylation-sites-in-proteins-by-incorporating-two-tiers-of-sequence-couplings-into-pseaac
#2
Yan Xu, Zu Wang, Chunhui Li, Kuo-Chen Chou
PURPOSE: Occurring at the cysteine residue in the C-terminal of a protein, prenylation is a special kind of post-translational modification (PTM), which may play a key role for statin in altering immune function. Therefore, knowledge of the prenylation sites in proteins is important for drug development as well as for in-depth understanding the biological process concerned. Given a query protein whose C-terminal contains some cysteine residues, which one can be of prenylation or none of them can be prenylated? METHODS: To address this problem, we have developed a new predictor, called "iPreny-PseAAC", by incorporating two tiers of sequence pair coupling effects into the general form of PseAAC (pseudo amino acid composition)...
April 19, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28418492/randomized-controlled-trial-in-clinical-settings-to-evaluate-effectiveness-of-coping-skills-education-used-with-progressive-tinnitus-management
#3
James A Henry, Emily J Thielman, Tara L Zaugg, Christine Kaelin, Caroline J Schmidt, Susan Griest, Garnett P McMillan, Paula Myers, Izel Rivera, Robert Baldwin, Kathleen Carlson
Purpose: This randomized controlled trial evaluated, within clinical settings, the effectiveness of coping skills education that is provided with progressive tinnitus management (PTM). Method: At 2 Veterans Affairs medical centers, N = 300 veterans were randomized to either PTM intervention or 6-month wait-list control. The PTM intervention involved 5 group workshops: 2 led by an audiologist (teaching how to use sound as therapy) and 3 by a psychologist (teaching coping skills derived from cognitive behavioral therapy)...
April 17, 2017: Journal of Speech, Language, and Hearing Research: JSLHR
https://www.readbyqxmd.com/read/28414281/-analysis-of-contribution-of-protein-phosphorylation-in-the-development-of-the-diseases
#4
REVIEW
M G Zavialova, V G Zgoda, E N Nikolaev
In recent decades, studies in the molecular origins of socially significant diseases have made a big step forward with the development and using of high-performance methods in genomics and proteomics. Numerous studies in the framework of the global program "Human Proteome" were aimed at the identification of all possible proteins in various cell cultures and tissues, including cancer. One of the objectives was to identify biomarkers - proteins with high specificity to certain pathologies. However, in many cases, it is shown that the development of the disease is not associated with the appearance of new proteins, but depends on the level of gene expression or forming of proteoforms - splice variants, single amino acid substitutions (SAP variants), and post-translational modifications (PTM) of proteins...
March 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
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/28409134/anatomical-variations-of-pronator-teres-muscle-predispositional-role-for-nerve-entrapment
#7
Edie Benedito Caetano, Luiz Ângelo Vieira, Fábio Antonio Anversa Sprovieri, Guilherme Camargo Petta, Maurício Tadeu Nakasone, Bárbara Lívia Correa Serafim
OBJECTIVE: To assess the anatomical variations of the pronator teres muscle (PTM) and its implication in the compression of the median nerve, which passes through the humeral and ulnar heads of the PTM. METHODS: For the present study, 100 upper limbs from human cadavers from the anatomy laboratory were dissected. Forty-six specimens were male and four, female, whose aged ranged from 28 to 77 years; 27 were white and 23, non-white. A pilot study consisting of six hands from three fresh cadaver dissections was conducted to familiarize the authors with the local anatomy; these were not included in the present study...
March 2017: Revista Brasileira de Ortopedia
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/28406606/characterization-of-complete-histone-tail-proteoforms-using-differential-ion-mobility-spectrometry
#9
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/28403192/a-novel-meloidogyne-graminicola-effector-mggpp-is-secreted-into-host-cells-and-undergoes-glycosylation-in-concert-with-proteolysis-to-suppress-plant-defenses-and-promote-parasitism
#10
Jiansong Chen, Borong Lin, Qiuling Huang, Lili Hu, Kan Zhuo, Jinling Liao
Plant pathogen effectors can recruit the host post-translational machinery to mediate their post-translational modification (PTM) and regulate their activity to facilitate parasitism, but few studies have focused on this phenomenon in the field of plant-parasitic nematodes. In this study, we show that the plant-parasitic nematode Meloidogyne graminicola has evolved a novel effector, MgGPP, that is exclusively expressed within the nematode subventral esophageal gland cells and up-regulated in the early parasitic stage of M...
April 12, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28396891/predicting-protein-lysine-phosphoglycerylation-sites-by-hybridizing-many-sequence-based-features
#11
Qing-Yun Chen, Jijun Tang, Pu-Feng Du
Post-translational modification (PTM) is essential for many biological processes. Covalent and generally enzymatic modification of proteins can impact the activity of proteins. Modified proteins would have more complex structures and functions. Knowing whether a specific residue is modified or not is significant to unravel the function and structure of this protein. As experimental approaches to discover protein PTM sites are always costly and time consuming, computational prediction methods are desirable alternative methods...
April 11, 2017: Molecular BioSystems
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
#12
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
#13
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/28385095/in-vitro-inhibitory-effects-of-pristimerin-on-human-liver-cytochrome-p450-enzymes
#14
Xiaoyi Hao, Jianlei Yuan, Yansen Xu, Zhao Wang, Jianzhang Hou, Tao Hu
1. Pristimerin (PTM) is a biological component isolated from Chinese herbal plant Celastrus and Maytenus spp and it possesses numerous pharmacological activities. However, whether PTM affects the activity of human liver cytochrome P450 (CYP) enzymes remains unclear. 2. In this study, the inhibitory effects of PTM on the eight human liver CYP isoforms (i.e., 1A2, 3A4, 2A6, 2E1, 2D6, 2C9, 2C19, and 2C8) were investigated in vitro using human liver microsomes (HLMs). 3. The results showed that PTM inhibited the activity of CYP1A2, 3A4, and 2C9, with IC50 values of 21...
April 7, 2017: Xenobiotica; the Fate of Foreign Compounds in Biological Systems
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
#15
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
#16
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
#17
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/28365727/curated-protein-information-in-the-saccharomyces-genome-database
#18
Sage T Hellerstedt, Robert S Nash, Shuai Weng, Kelley M Paskov, Edith D Wong, Kalpana Karra, Stacia R Engel, J Michael Cherry
Due to recent advancements in the production of experimental proteomic data, the Saccharomyces genome database (SGD; www.yeastgenome.org ) has been expanding our protein curation activities to make new data types available to our users. Because of broad interest in post-translational modifications (PTM) and their importance to protein function and regulation, we have recently started incorporating expertly curated PTM information on individual protein pages. Here we also present the inclusion of new abundance and protein half-life data obtained from high-throughput proteome studies...
January 1, 2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28363440/sucstruct-prediction-of-succinylated-lysine-residues-by-using-structural-properties-of-amino-acids
#19
Yosvany López, Abdollah Dehzangi, Sunil Pranit Lal, Ghazaleh Taherzadeh, Jacob Michaelson, Abdul Sattar, Tatsuhiko Tsunoda, Alok Sharma
Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming...
March 28, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28361707/investigation-and-identification-of-protein-carbonylation-sites-based-on-position-specific-amino-acid-composition-and-physicochemical-features
#20
Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu, Tzong-Yi Lee
BACKGROUND: Protein carbonylation, an irreversible and non-enzymatic post-translational modification (PTM), is often used as a marker of oxidative stress. When reactive oxygen species (ROS) oxidized the amino acid side chains, carbonyl (CO) groups are produced especially on Lysine (K), Arginine (R), Threonine (T), and Proline (P). Nevertheless, due to the lack of information about the carbonylated substrate specificity, we were encouraged to develop a systematic method for a comprehensive investigation of protein carbonylation sites...
March 14, 2017: BMC Bioinformatics
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