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https://www.readbyqxmd.com/read/28636386/msviz-a-graphical-software-tool-for-in-depth-manual-validation-and-quantitation-of-post-translational-modifications
#1
Trinidad Martin Campos, Roman Mylonas, Alexandre Masselot, Patrice Waridel, Tanja Petricevic, Ioannis Xenarios, Manfredo Quadroni
Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTM's of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation...
June 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28628292/an-environment-sensitive-turn-on-fluorescent-polyamino-acid-fingerprinting-protein-populations-with-post-translational-modifications
#2
Shunsuke Tomita, Sayaka Ishihara, Ryoji Kurita
The identification of post-translational modifications (PTMs) in proteins has been of particular interest in the elucidation of human diseases and the improvement of therapeutic proteins. Herein, we report a novel strategy toward the construction of fingerprint-based PTM sensing systems as an alternative to conventional specific recognition tools. Our strategy is based on poly-L-lysine (PLL) derivatives with two distinct properties suitable to fingerprint-based protein sensing: i) a "turn-on" fluorescent signal upon binding to proteins, and ii) condition-dependent cross-reactivity toward proteins and PTMs...
June 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28626267/a-facile-semi-synthetic-approach-towards-halogen-substituted-aminobenzoic-acid-analogues-of-platensimycin
#3
Lin Qiu, Kai Tian, Jian Pan, Lin Jiang, Hu Yang, Xiangcheng Zhu, Ben Shen, Yanwen Duan, Yong Huang
Platensimycin (PTM), produced by several strains of Streptomyces platensis, is a promising drug lead for infectious diseases and diabetes. The recent pilot-scale production of PTM from S. platensis SB12026 has set the stage for the facile semi-synthesis of a focused library of PTM analogues. In this study, gram-quantity of platensic acid (PTMA) was prepared by the sulfuric acid-catalyzed ethanolysis of PTM, followed by a mild hydrolysis in aqueous lithium hydroxide. Three PTMA esters were also obtained in near quantitative yields in a single step, suggesting a facile route to make PTMA aliphatic esters...
February 9, 2017: Tetrahedron
https://www.readbyqxmd.com/read/28615324/hihimap-single-cell-quantitation-of-histones-and-histone-post-translational-modifications-across-the-cell-cycle-by-high-throughput-imaging
#4
Linda Zane, Fleur Chapus, Gianluca Pegoraro, Tom Misteli
We describe HiHiMap (High-throughput Histone Mapping), a high-throughput imaging method to measure histone and histone post-translational modifications (PTM) in single cells. HiHiMap uses imaging-based quantification of DNA and Cyclin A to stage individual cells in the cell cycle to determine the levels of histone or histone PTMs in each stage of the cell cycle. As proof-of-principle, we apply HiHiMap to measure the level of 21 core histones, histone variants and PTMs in primary, immortalized and transformed cells...
June 14, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28606917/quantitative-temporal-viromics-of-an-inducible-hiv-1-model-yields-insight-to-global-host-targets-and-phospho-dynamics-associated-with-vpr
#5
John D Lapek, Mary K Lewinski, Jacob M Wozniak, John Guatelli, David J Gonzalez
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist...
June 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28594096/ttf-ptm-dyads-the-role-of-the-bridge-and-open-shell-character-on-the-linear-and-nonlinear-optical-properties
#6
Jaume Veciana, Manuel Souto, Joaquin Calbo, Imma Ratera, Enrique Ortí
In this article, three conjugated donor-Π-acceptor radical systems (1a-1c) based on a tetrathiafulvalene (TTF) unit, as electron-donor, connected to a polychlorotriphenylmethyl (PTM) radical, as electron-acceptor, through different vinylene units as bridge have been synthesized. The dependence of the intramolecular charge transfer on the length of the conjugated bridge has been analysed by different electrochemical and spectroscopic techniques. In addition, linear optical properties and the second-order non-linear optical (NLO) response of these derivatives have been theoretically calculated by comparing with their non-radical analogues (2a-2c)...
June 8, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28592803/first-comprehensive-proteome-analysis-of-lysine-crotonylation-in-seedling-leaves-of-nicotiana-tabacum
#7
Hangjun Sun, Xiaowei Liu, Fangfang Li, Wei Li, Jing Zhang, Zhixin Xiao, Lili Shen, Ying Li, Fenglong Wang, Jinguang Yang
Histone crotonylation is a new lysine acylation type of post-translational modification (PTM) enriched at active gene promoters and potential enhancers in yeast and mammalian cells. However, lysine crotonylation in nonhistone proteins and plant cells has not yet been studied. In the present study, we performed a global crotonylation proteome analysis of Nicotiana tabacum (tobacco) using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity purification. A total of 2044 lysine modification sites distributed on 637 proteins were identified, representing the most abundant lysine acylation proteome reported in the plant kingdom...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28575669/the-mammalian-ribo-interactome-reveals-ribosome-functional-diversity-and-heterogeneity
#8
Deniz Simsek, Gerald C Tiu, Ryan A Flynn, Gun W Byeon, Kathrin Leppek, Adele F Xu, Howard Y Chang, Maria Barna
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes...
June 1, 2017: Cell
https://www.readbyqxmd.com/read/28570536/isolation-of-intermediate-filament-proteins-from-multiple-mouse-tissues-to-study-aging-associated-post-translational-modifications
#9
Rachel A Battaglia, Parijat Kabiraj, Helen H Willcockson, Melinda Lian, Natasha T Snider
Intermediate filaments (IFs), together with actin filaments and microtubules, form the cytoskeleton - a critical structural element of every cell. Normal functioning IFs provide cells with mechanical and stress resilience, while a dysfunctional IF cytoskeleton compromises cellular health and has been associated with many human diseases. Post-translational modifications (PTMs) critically regulate IF dynamics in response to physiological changes and under stress conditions. Therefore, the ability to monitor changes in the PTM signature of IFs can contribute to a better functional understanding, and ultimately conditioning, of the IF system as a stress responder during cellular injury...
May 18, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28559875/beyond-the-impasse-reflections-on-dissociative-identity-disorder-from-a-freudian-lacanian-perspective
#10
Reitske Meganck
Dissociative identity disorder (DID) is a widely contested diagnosis. The dominant posttraumatic model (PTM) considers early life trauma to be the direct cause of the creation of alter identities and assumes that working directly with alter identities should be at the core of the therapeutic work. The socio-cognitive model, on the other hand, questions the validity of the DID diagnosis and proposes an iatrogenic origin of the disorder claiming that reigning therapeutic and socio-cultural discourses create and reify the problem...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28558143/parsing-disease-relevant-protein-modifications-from-epiphenomena-perspective-on-the-structural-basis-of-sod1-mediated-als
#11
N D Schmitt, J N Agar
Conformational change and modification of proteins are involved in many cellular functions. However, they can also have adverse effects that are implicated in numerous diseases. How structural change promotes disease is generally not well understood. This perspective illustrates how mass spectrometry (MS), followed by toxicological and epidemiological validation, can discover disease-relevant structural changes and therapeutic strategies. We (with our collaborators) set out to characterize the structural and toxic consequences of disease-associated mutations and post-translational modifications (PTMs) of the cytosolic antioxidant protein Cu/Zn-Superoxide dismutase (SOD1)...
May 30, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28553538/site-selective-reading-of-epigenetic-markers-by-a-dual-mode-synthetic-receptor-array
#12
Yang Liu, Lizeth Perez, Magi Mettry, Adam D Gill, Samantha R Byers, Connor J Easley, Christopher J Bardeen, Wenwan Zhong, Richard J Hooley
Variably functionalized self-folding deep cavitands form an arrayed, fluorescent indicator displacement assay system for the detection of post-translationally modified (PTM) histone peptides. The hosts bind trimethyllysine (KMe3) groups, and use secondary upper rim interactions to provide more sensitive discrimination between targets with identical KMe3 binding handles. The sensor array uses multiple different recognition modes to distinguish between miniscule differences in target, such as identical lysine modifications at different sites of histone peptides...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28538164/post-translational-regulation-of-plant-immunity
#13
REVIEW
John Withers, Xinnian Dong
Plants have evolved multi-layered molecular defense strategies to protect against pathogens. Plant immune signaling largely relies on post-translational modifications (PTMs) to induce rapid alterations of signaling pathways to achieve a response that is appropriate to the type of pathogen and infection pressure. In host cells, dynamic PTMs have emerged as powerful regulatory mechanisms that cells use to adjust their immune response. PTM is also a virulence strategy used by pathogens to subvert host immunity through the activities of effector proteins secreted into the host cell...
May 21, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28537252/an-hsp90-co-chaperone-protein-in-yeast-is-functionally-replaced-by-site-specific-posttranslational-modification-in-humans
#14
Abbey D Zuehlke, Michael Reidy, Coney Lin, Paul LaPointe, Sarah Alsomairy, D Joshua Lee, Genesis M Rivera-Marquez, Kristin Beebe, Thomas Prince, Sunmin Lee, Jane B Trepel, Wanping Xu, Jill Johnson, Daniel Masison, Len Neckers
Heat shock protein 90 (Hsp90) is an essential eukaryotic molecular chaperone. To properly chaperone its clientele, Hsp90 proceeds through an ATP-dependent conformational cycle influenced by posttranslational modifications (PTMs) and assisted by a number of co-chaperone proteins. Although Hsp90 conformational changes in solution have been well-studied, regulation of these complex dynamics in cells remains unclear. Phosphorylation of human Hsp90α at the highly conserved tyrosine 627 has previously been reported to reduce client interaction and Aha1 binding...
May 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534629/synthetic-posttranslational-modifications-chemical-catalyst-driven-regioselective-histone-acylation-of-native-chromatin
#15
Yoshifumi Amamoto, Yuki Aoi, Nozomu Nagashima, Hiroki Suto, Daisuke Yoshidome, Yasuhiro Arimura, Akihisa Osakabe, Daiki Kato, Hitoshi Kurumizaka, Shigehiro A Kawashima, Kenzo Yamatsugu, Motomu Kanai
Posttranslational modifications (PTMs) of histones play an important role in the complex regulatory mechanisms governing gene transcription, and their dysregulation can cause diseases such as cancer. The lack of methods for site-selectively modifying native chromatin, however, limits our understanding of the functional roles of a specific histone PTM, not as a single mark, but in the intertwined PTM network. Here, we report a synthetic catalyst DMAP-SH (DSH), which activates chemically stable thioesters (including acetyl-CoA) under physiological conditions and transfers various acyl groups to the proximate amino groups...
June 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28525809/one-step-preparation-of-nanostructured-martite-catalyst-and-graphite-electrode-by-glow-discharge-plasma-for-heterogeneous-electro-fenton-like-process
#16
Alireza Khataee, Saeed Sajjadi, Aliyeh Hasanzadeh, Behrouz Vahid, Sang Woo Joo
Natural Martite ore particles and graphite were modified by alternating current (AC) glow discharge plasma to form nanostructured catalyst and cathode electrode for using in the heterogeneous-electro Fenton-like (Het-EF-like) process. The performance of the plasma-treated martite (PTM) and graphite electrode (PTGE) was studied for the treatment of paraquat herbicide in a batch system. 85.78% degradation efficiency for 20 mg L(-1) paraquat was achieved in the modified process under desired operational conditions (i...
September 1, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28521678/ipgk-pseaac-identify-lysine-phosphoglycerylation-sites-in-proteins-by-incorporating-four-different-tiers-of-amino-acid-pairwise-coupling-information-into-the-general-pseaac
#17
Li-Ming Liu, Yan Xu, Kuo-Chen Chou
BACKGROUND: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney. OBJECTIVE: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot? METHOD: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively...
May 15, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28520665/family-history-of-migraine-associated-with-posttraumatic-migraine-symptoms-following-sport-related-concussion
#18
Alicia Sufrinko, Jamie McAllister-Deitrick, R J Elbin, Michael W Collins, Anthony P Kontos
OBJECTIVE: To determine whether family history of migraine increased the likelihood of posttraumatic migraine (PTM) symptom presentation in adolescents following concussion, and examine the influence of family history of migraine and PTM on postinjury outcomes. SETTING: Outpatient concussion clinic. PARTICIPANTS: A total of 153 patients with concussion (103 males and 50 females) aged 15.72 ± 1.48 years (range 12-18 years). DESIGN: Cross-sectional, observational study of patients presenting for initial evaluation 4...
May 17, 2017: Journal of Head Trauma Rehabilitation
https://www.readbyqxmd.com/read/28508372/effect-of-second-hand-tobacco-smoke-on-the-nitration-of-brain-proteins-a-systems-biology-and-bioinformatics-approach
#19
Firas H Kobeissy, Joy Guingab-Cagmat, Adriaan W Bruijnzeel, Mark S Gold, Kevin Wang
Second-hand smoke (SHS) exposure leads to the death of approximately 48,000 nonsmokers per year in the United States alone. SHS exposure has been associated with cardiovascular, respiratory, and neurodegenerative diseases. While cardiac function abnormalities and lung cancer due to SHS have been well characterized, brain injury due to SHS has not undergone a full systematic evaluation. Oxidative stress and nitration have been associated with smoking and SHS exposure. Animal studies suggest that exposure to tobacco smoke increases oxidative stress...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28505447/interrogating-the-roles-of-post-translational-modifications-of-non-histone-proteins
#20
Zakey Yusuf Buuh, Zhigang Lyu, Rongsheng E Wang
Post-translational modifications (PTMs) allot versatility to the biological functions of highly conserved proteins. Recently, modifications to non-histone proteins such as methylation, acetylation, phosphorylation, glycosylation, ubiquitination, and many more have been linked to the regulation of pivotal pathways related to cellular response and stability. Due to the roles these dynamic modifications assume, their dysregulation has been associated with cancer and many other important diseases such as inflammatory disorders and neurodegenerative diseases...
May 15, 2017: Journal of Medicinal Chemistry
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