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Brian McDonagh
Reversible and irreversible post-translational modifications (PTMs) induced by endogenously generated reactive oxygen species (ROS) in regulatory enzymes and proteins plays an essential role in cellular signaling. Almost all cellular processes including metabolism, transcription, translation and degradation have been identified as containing redox regulated proteins. Specific redox modifications of key amino acids generated by ROS offers a dynamic and versatile means to rapidly alter the activity or functional structure of proteins in response to biochemical, environmental, genetic and pathological perturbations...
2017: Frontiers in Physiology
Zhifeng Wang, Wei-Guo Zhu, Xingzhi Xu
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1)...
July 11, 2017: Mutation Research
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
Henrick Horita, Andy Law, Soonjin Hong, Kim Middleton
Identification of a novel post-translational modification (PTM) for a target protein, defining its physiologic role, and studying its potential crosstalk with other PTMs is a challenging process. A set of highly sensitive tools termed Signal-Seeker kits was developed, which enables rapid and simple detection of post-translational modifications on any target protein.  The methodology for these tools utilizes affinity purification of modified proteins from a cell or tissue lysate and immunoblot analysis. These tools utilize a single lysis system that is effective at identifying endogenous, dynamic PTM changes, as well as the potential crosstalk between PTMs...
July 19, 2017: Bioscience Reports
Anett Hauser, Martin Penkert, Christian P R Hackenberger
Protein phosphorylation is by far the most abundant and most studied post-translational modification (PTM). For a long time, phosphate monoesters of serine (pSer), threonine (pThr), and tyrosine (pTyr) have been considered as the only relevant forms of phosphorylation in organisms. Recently, several research groups have dedicated their efforts to the investigation of other, less characterized phosphoamino acids as naturally occurring PTMs. Such apparent peculiar phosphorylations include the phosphoramidates of histidine (pHis), arginine (pArg), and lysine (pLys), the phosphorothioate of cysteine (pCys), and the anhydrides of pyrophosphorylated serine (ppSer) and threonine (ppThr)...
July 19, 2017: Accounts of Chemical Research
Xinpeng Fu, Fangfei Li, Jung-Fu Lin, Yuan-Bo Gong, Xiaoli Huang, Yanping Huang, Bo Han, Qiang Zhou, Tian Cui
Tailoring the excitonic properties in two-dimensional monolayer transition metal dichalcogenides (TMDs) through strain engineering is an effective means to explore their potential applications in optoelectronics and nanoelectronics. Here we report pressure-tuned photon emission of trions and excitons in monolayer MoSe2 via a diamond anvil cell (DAC) through photoluminescence measurements and theoretical calculations. Under quasi-hydrostatic compressive strain, our results show neutral (X0) and charged (X-) excitons emission of monolayer MoSe2 can be effectively tuned by alcohol mixture vs...
July 17, 2017: Journal of Physical Chemistry Letters
Karen E Ross, Darren A Natale, Cecilia Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K Vijay-Shanker, Cathy H Wu
The Protein Ontology (PRO) defines protein classes and their interrelationships from the family to the protein form (proteoform) level within and across species. One of the unique contributions of PRO is its representation of post-translationally modified (PTM) proteoforms. However, progress in adding PTM proteoform classes to PRO has been relatively slow due to the extensive manual curation effort required. Here we report an automated pipeline for creation of PTM proteoform classes that leverages two phosphorylation-focused text mining tools (RLIMS-P, which detects mentions of kinases, substrates, and phosphorylation sites, and eFIP, which detects phosphorylation-dependent protein-protein interactions (PPIs)) and our integrated PTM database, iPTMnet...
August 2016: CEUR Workshop Proceedings
Kelly A Hyndman, Mark A Knepper
Reversible posttranslational modification (PTM) of proteins is a critically important process in physiological regulation in all tissues including the kidney. Lysine acetylation occurs in all organisms including prokaryotes, and is regulated by a balance between the lysine acetyltransferases (adding an acetyl group to the ε-amino group of a lysine) and deacetylases (removing it). The kidney is an organ rich with acetylated lysines which map to >2000 unique histone and non-histone proteins. However, the functional significance of these modifications remains to be discovered...
July 12, 2017: American Journal of Physiology. Renal Physiology
Sara C Larsen, Mario Leutert, Vera Bilan, Rita Martello, Stephanie Jungmichel, Clifford Young, Michael O Hottiger, Michael L Nielsen
ADP-ribosylation is a posttranslational modification (PTM) that affects a variety of cellular processes. In recent years, mass spectrometry (MS)-based proteomics has become a valuable tool for studying ADP-ribosylation. However, studying this PTM in vivo in an unbiased and sensitive manner has remained a difficult challenge. Here, we describe a detailed protocol for unbiased analysis of ADP-ribosylated proteins and their ADP-ribose acceptor sites under physiological conditions. The method relies on the enrichment of mono-ADP-ribosylated peptides using the macrodomain Af1521 in combination with liquid chromatography-high-resolution tandem MS (LC-MS/MS)...
2017: Methods in Molecular Biology
Mario Leutert, Vera Bilan, Peter Gehrig, Michael O Hottiger
Protein ADP-ribosylation is a covalent, reversible posttranslational modification (PTM) catalyzed by ADP-ribosyltransferases (ARTs). Proteins can be either mono- or poly-ADP-ribosylated under a variety of physiological and pathological conditions. To understand the functional contribution of protein ADP-ribosylation to normal and disease/stress states, modified protein and corresponding ADP-ribose acceptor site identification is crucial. Since ADP-ribosylation is a transient and relatively low abundant PTM, systematic and accurate identification of ADP-ribose acceptor sites has only recently become feasible...
2017: Methods in Molecular Biology
Casey M Daniels, Shao-En Ong, Anthony K L Leung
Protein ADP-ribosylation is a posttranslational modification (PTM) that plays an important role in all major cellular processes, including DNA repair, cellular signaling, and RNA metabolism. Site identification for this PTM has recently become possible through the development of several mass spectrometry-based methods, a critical step in understanding the regulatory role played by mono(ADP-ribose) (MAR), poly(ADP-ribose) (PAR), and the enzymes which make these modifications: poly(ADP-ribose) polymerases (PARPs), best known for their role in DNA repair and as targets for chemotherapeutic PARP inhibitors...
2017: Methods in Molecular Biology
Maria Hernandez-Valladares, Marc Vaudel, Frode Selheim, Frode Berven, Øystein Bruserud
Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases,proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples. Areas covered: Proteogenomics involves the understanding of genomic and proteomic data...
July 11, 2017: Expert Review of Proteomics
Cheng-Chih Hsu, Michael W Baker, Terry Gaasterland, Michael J Meehan, Eduardo R Macagno, Pieter C Dorrestein
Mass spectrometry-based protein analysis has become an important methodology for proteogenomic mapping by providing evidence for the existence of proteins predicted at the genomic level. However, screening and identification of proteins directly on tissue samples, where histological information is preserved, remain challenging. Here we demonstrate that the ambient ionization source, nanospray desorption electrospray ionization (nanoDESI), interfaced with light microscopy allows for protein profiling directly on animal tissues at the microscopic scale...
July 24, 2017: Analytical Chemistry
Rong Zhang, Weizhao Cai, Tiange Bi, Niloofar Zarifi, Tyson Terpstra, Chuang Zhang, Zeev Valy Vardeny, Eva Zurek, Shanti Deemyad
We report synchrotron X-ray diffraction, photoconductivity and photoluminescence investigations of methylammonium-lead-bromide (MAPbBr3) under various stress conditions, supported by density-functional-theory (DFT) calculations. MAPbBr3 shows substantial dependence on the hydrostatic conditions. While non-hydrostatic compression of MAPbBr3 leads to amorphization above 2.4GPa, under quasi-hydrostatic (Ar) and hydrostatic (He) pressure the sample remains in crystalline phases. Sequence of phase transitions between two cubic phases (Pm3 ̅m and Im3 ̅) and orthorhombic Pnma phase is observed when using Ar, or no pressure-transmitting-medium (PTM)...
July 10, 2017: Journal of Physical Chemistry Letters
Shweta Bhat, Mashanipalya G Jagadeeshaprasad, Vinashya Venkatasubramani, Mahesh J Kulkarni
Human serum albumin (HSA) is a multifaceted protein with vital physiological functions. It is the most abundant plasma protein with inherent capability to bind to diverse ligands, and thus susceptible to various post-translational modifications (PTMs) which alter its structure and functions. One such PTM is glycation, a non-enzymatic reaction between reducing sugar and protein leading to formation of heterogeneous advanced glycation end products (AGEs). Glycated albumin (GA) concentration increases significantly in diabetes and is implicated in development of secondary complications...
July 10, 2017: Expert Review of Proteomics
Nilesh Zaware, Ming-Ming Zhou
Site-specific lysine acetylation and methylation on histones are critical post-translational modifications (PTMs) that govern ordered gene transcription in chromatin. Mis-regulation of these histone PTM-mediated processes has been shown to be associated with human diseases. Since the 2010 landmark reports of small molecules (+)-JQ1 and I-BET762 that target the acetyl-lysine 'reader' Bromodomain and Extra Terminal domain (BET) proteins, there have been relentless efforts to develop epigenetic therapy with small molecules to modulate molecular interactions of epigenome reader domain proteins with PTMs...
July 6, 2017: Current Opinion in Chemical Biology
Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R Karch, Chrystian Ruminowicz, Benjamin A Garcia
BACKGROUND: Middle-down mass spectrometry (MS), i.e., analysis of long (~50-60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities...
July 6, 2017: Epigenetics & Chromatin
Xue Zhang, Peng Liu, Christie Zhang, Direkrit Chiewchengchol, Fan Zhao, Hongbo Yu, Jingyu Li, Hiroto Kambara, Kate Y Luo, Arvind Venkataraman, Ziling Zhou, Weidong Zhou, Haiyan Zhu, Li Zhao, Jiro Sakai, Yuanyuan Chen, Ye-Shih Ho, Besnik Bajrami, Bing Xu, Leslie E Silberstein, Tao Cheng, Yuanfu Xu, Yuehai Ke, Hongbo R Luo
Reactive oxygen species (ROS)-induced cysteine S-glutathionylation is an important posttranslational modification (PTM) that controls a wide range of intracellular protein activities. However, whether physiological ROS can modulate the function of extracellular components via S-glutathionylation is unknown. Using a screening approach, we identified ROS-mediated cysteine S-glutathionylation on several extracellular cytokines. Glutathionylation of the highly conserved Cys-188 in IL-1β positively regulates its bioactivity by preventing its ROS-induced irreversible oxidation, including sulfinic acid and sulfonic acid formation...
July 5, 2017: Cell Reports
Jiaming Zhang, Haozhi Lei, Yubei Chen, Yan-Tao Ma, Fang Jiang, Jieqiong Tan, Yi Zhang, Jia-Da Li
Neurodegenerative diseases including dementia with Lewy bodies, Lewy body variant of Alzheimer's disease, and Parkinson's disease are associated with the aberrant aggregation of α-synuclein, which is influenced by several post-translational modifications (PTMs). O-GlcNAcylation is one PTM that has an important role in many fundamental processes. The O-GlcNAcylation of endogenous α-synuclein at residues 53, 64, 72 and 87 has been reported in an unbiased mass spectrum analysis. The consequences of O-GlcNAcylation at residues 72 or 87 have been studied by using a synthetic α-synuclein bearing O-GlcNAcylation at threonine residue 72 or serine 87, respectively...
July 1, 2017: Neuroscience Letters
James A Henry, Emily Thielman, Tara Zaugg, Christine Kaelin, Christie Choma, Bill Chang, Shira Hahn, Bret Fuller
OBJECTIVE: This study's objective was to develop and test a smartphone app that supports learning and using coping skills for managing tinnitus. DESIGN: The app's content was based on coping skills that are taught as a part of progressive tinnitus management (PTM). The study involved three phases: (1) develop a prototype app and conduct usability testing; (2) conduct two focus groups to obtain initial feedback from individuals representing potential users; and (3) conduct a field study to evaluate the app, with three successive groups of participants...
July 2, 2017: International Journal of Audiology
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