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Sandra Martínez-Turiño, José de Jesús Pérez, Marta Hervás, Rosana Navajas, Sergio Ciordia, Namrata D Udeshi, Jeffrey Shabanowitz, Donald F Hunt, Juan Antonio García
Phosphorylation and O-GlcNAcylation are two widespread post-translational modifications (PTM), often affecting the same eukaryotic target protein. Plum pox virus (PPV) is a member of the genus Potyvirus that infects a wide range of plant species. O-GlcNAcylation of the capsid protein (CP) of PPV has been extensively studied, and some evidence about CP phosphorylation has been additionally reported. Here, we use proteomics analyses to demonstrate that PPV CP is phosphorylated in vivo at the N-terminus and the beginning of the core region...
October 11, 2017: Molecular Plant Pathology
Mariana Duarte, Prabal Subedi, Ecevit Yilmaz, Katrin Marcus, Thomas Laurell, Simon Ekström
Phosphorylation is a protein post-translational modification (PTM) that plays an important role in cell signaling, cell differentiation, and metabolism. The hyper phosphorylated forms of certain proteins have been appointed as biomarkers for neurodegenerative diseases, and phosphorylation-related mutations are important for detecting cancer pathways. Due to the low abundance of phosphorylated proteins in biological fluids, sample enrichment is beneficial prior to detection. Thus, a need to find new strategies for enriching phosphopeptides has emerged...
October 12, 2017: Journal of Molecular Recognition: JMR
Tian Qiu, Rahul S Kathayat, Yang Cao, Michael William Beck, Bryan C Dickinson
S-palmitoylation is an abundant lipid post-translational modification (PTM) that is dynamically installed on and removed from target proteins to regulate their activity and cellular localization. A dearth of tools to study the activities and regulation of protein S-depalmitoylases - thioesterase "erasers" of protein cysteine S-palmitoylation - has contributed to an incomplete understanding of the role of dynamic S-palmitoylation in regulating proteome lipidation. Recently, we developed "depalmitoylation probes" (DPPs), small molecule probes that become fluorescent upon S-depalmitoylase enzymatic activity...
October 12, 2017: Biochemistry
Faisal Alnemary, Michele Wallace, Fahad Alnemary, Lusineh Gharapetian, Jordan Yassine
We employed a pyramidal training model (PTM) to teach staff to correctly implement and collect data for trial-based functional analysis (TBFA) in simulated situations. First, we trained four behavioral consultants (BCs) in a group format, who each trained one behavior technician (BT) in an individual format. We utilized a non-concurrent multiple baseline design to evaluate the effect of the training. During generalization probes, participants implemented TBFA with a novel problem behavior. This study will contribute to the literature on teaching staff how to conduct TBFA...
September 2017: Behavior Analysis in Practice
Stephanie Munk, Jón Otti Sigurðsson, Zhenyu Xiao, Tanveer Singh Batth, Giulia Franciosa, Louise von Stechow, Andres Joaquin Lopez-Contreras, Alfred Cornelis Otto Vertegaal, Jesper Velgaard Olsen
The mechanisms that protect eukaryotic DNA during the cumbersome task of replication depend on the precise coordination of several post-translational modification (PTM)-based signaling networks. Phosphorylation is a well-known regulator of the replication stress response, and recently an essential role for SUMOs (small ubiquitin-like modifiers) has also been established. Here, we investigate the global interplay between phosphorylation and SUMOylation in response to replication stress. Using SUMO and phosphoproteomic technologies, we identify thousands of regulated modification sites...
October 10, 2017: Cell Reports
Daniel A Plymire, Casey Elizabeth Wing, Dana E Robinson, Steven Patrie
Myelin basic protein (MBP) plays an important structural and functional role in the neuronal myelin sheath. Translated MBP exhibits extreme microheterogeneity with numerous alternative splice variants (ASVs) and post- translational modifications (PTMs) reportedly tied to central nervous system maturation, myelin stability, and the pathobiology of various de- and dys-myelinating disorders. Conventional bioanalytical tools cannot efficiently examine ASV and PTM events simultaneously which limits understanding of the role of MBP microheterogeneity in human physiology and disease...
October 10, 2017: Analytical Chemistry
Jishan Wu, Xiao Gu, Tullimilli Y Gopalakrishna, Hoa Phan, Yong Ni, Tun Seng Herng, Jun Ding
π-Conjugated molecular cages are very challenging targets in structural organic chemistry, supramolecular chemistry and materials science. Herein, we report the synthesis and physical characterizations of the first three-dimensionally π-conjugated diradical molecular cage PTM-C, in which two polychlorotriphenylmethyl (PTM) radicals are linked by three bis(3,6-carbazolyl) bridges. This cage compound was synthesized mainly by intermolecular Yamamoto coupling followed by deprotonation and oxidation. It is stable and its structure was confirmed by X-ray crystallographic analysis...
October 10, 2017: Angewandte Chemie
László Imre, Zoltán Simándi, Attila Horváth, György Fenyőfalvi, Péter Nánási, Erfaneh Firouzi Niaki, Éva Hegedüs, Zsolt Bacsó, Urbain Weyemi, Rebekka Mauser, Juan Ausio, Albert Jeltsch, William Bonner, László Nagy, Hiroshi Kimura, Gábor Szabó
Current approaches have limitations in providing insight into the functional properties of particular nucleosomes in their native molecular environment. Here we describe a simple and powerful method involving elution of histones using intercalators or salt, to assess stability features dependent on DNA superhelicity and relying mainly on electrostatic interactions, respectively, and measurement of the fraction of histones remaining chromatin-bound in the individual nuclei using histone type- or posttranslational modification- (PTM-) specific antibodies and automated, quantitative imaging...
October 6, 2017: Scientific Reports
Louise C Bryan, Daniel R Weilandt, Andreas L Bachmann, Sinan Kilic, Carolin C Lechner, Pascal D Odermatt, Georg E Fantner, Sandrine Georgeon, Oliver Hantschel, Vassily Hatzimanikatis, Beat Fierz
Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is currently not understood how effectors dynamically sample the chromatin landscape. Here, we dissect the dynamic chromatin interactions of a family of multivalent effectors, heterochromatin protein 1 (HP1) proteins, using single-molecule fluorescence imaging and computational modeling...
August 3, 2017: Nucleic Acids Research
Oluwatosin O Dada, Yimeng Zhao, Nomalie Jaya, Oscar Salas-Solano
RPLC-MS peptide mapping is routinely used for interrogating molecular and structural attributes such as amino acid composition, sequence variants, and post translational modifications (PTMs) in antibody derived therapeutics. RPLC has some limitations that often impact the analysis of certain peptides including large hydrophobic peptides, hydrophilic di/tri-peptides and glycopeptides. Capillary zone electrophoresis with mass spectrometry (CZE-MS) has great potential for peptide mapping due to high efficiency and outstanding sensitivity...
October 6, 2017: Analytical Chemistry
Dongdong Sun, Minghui Wang, Ao Li
Due to the importance of post-translational modifications (PTMs) in human health and diseases, PTMs are regularly reported in the biomedical literature. However, the continuing and rapid pace of expansion of this literature brings a huge challenge for researchers and database curators. Therefore, there is a pressing need to aid them in identifying relevant PTM information more efficiently by using a text mining system. So far, only a few web servers are available for mining information of a very limited number of PTMs, which are based on simple pattern matching or pre-defined rules...
October 2017: Journal of Bioinformatics and Computational Biology
Mohammad A Halim, Luke MacAleese, Jérôme Lemoine, Rodolphe Antoine, Philippe Dugourd, Marion Girod
Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations...
October 4, 2017: Journal of the American Society for Mass Spectrometry
Nicolas Arbez, Tamara Ratovitski, Elaine Roby, Ekaterine Chighladze, Jacqueline Stewart, Mark Ren, Xiaofang Wang, Daniel J Lavery, Christopher A Ross
Huntington's disease (HD) is caused in large part by a polyglutamine expansion within the huntingtin (Htt) protein. Posttranslational modifications (PTMs) control and regulate many protein functions and cellular pathways, and PTMs of mutant Htt are likely important modulators of HD pathogenesis. Alterations of a selected numbers of PTMs of Htt fragments have been shown to modulate Htt cellular localization and toxicity. In this study, we systematically introduced site-directed alterations in individual phosphorylation and acetylation sites in full-length Htt constructs...
September 27, 2017: Journal of Biological Chemistry
Yunxiang Dai, Michael R Shortreed, Mark Scalf, Brian L Frey, Anthony J Cesnik, Stefan Solntsev, Leah V Schaffer, Lloyd M Smith
A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each proteoform: i) the accurate proteoform intact-mass, measured by liquid chromatography/mass spectrometry (LC-MS), and ii) the number of lysine residues in each proteoform, determined using an isotopic labeling approach...
October 2, 2017: Journal of Proteome Research
Shigeo Hayakawa
High energy collision processes for singly charged positive ions using an alkali metal target are confirmed, as a charge inversion mass spectrometry, to occur by electron transfers in successive collisions and the dissociation processes involve the formation of energy-selected neutral species from near-resonant neutralization with alkali metal targets. A doubly charged thermometer molecule was made to collide with alkali metal targets to give singly and doubly charged positive ions. The internal energy resulting from the electron transfer with the alkali metal target was very narrow and centered at a particular energy...
2017: Mass Spectrometry
Jingxuan Zhu, Yishuo Lv, Xiaosong Han, Dong Xu, Weiwei Han
ADP-ribosylhydrolases (ARH1, ARH2 and ARH3) are a family of enzymes to catalyze ADP-ribosylation, a reversible and covalent post-translational modification (PTM). There are four phosphorylated sites (Tyr-4, Tyr-19, Tyr-20, and Tyr-205) in ARH1. To explore the structural changes and functional impact induced by phosphorylation, molecular dynamics (MD) simulations and steered molecular dynamics (SMD) simulations were performed for the phosphorylated and non-phosphorylated ARH1 with the ligands. MD simulations results indicate that: (1) Glu-25 is more frequently in the α helix group in the phosphorylated state with the adenosine-5-diphosphate-ribosylarginine (ADP-RA) complex (51...
September 29, 2017: Scientific Reports
Yang Guo, Chaochao Dun, Junwei Xu, Jiuke Mu, Peiyun Li, Liwen Gu, Chengyi Hou, Corey A Hewitt, Qinghong Zhang, Yaogang Li, David L Carroll, Hongzhi Wang
Freestanding, flexible/foldable, and wearable bifuctional ultrathin graphene paper for heating and cooling is fabricated as an active material in personal thermal management (PTM). The promising electrical conductivity grants the superior Joule heating for extra warmth of 42 °C using a low supply voltage around 3.2 V. Besides, based on its high out-of-plane thermal conductivity, the graphene paper provides passive cooling via thermal transmission from the human body to the environment within 7 s. The cooling effect of graphene paper is superior compared with that of the normal cotton fiber, and this advantage will become more prominent with the increased thickness difference...
September 29, 2017: Small
Yihao Wang, Yang Chen, Yao Zhang, Wei Wei, Yanchang Li, Tao Zhang, Fuchu He, Yue Gao, Ping Xu
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin...
October 13, 2017: Journal of Proteome Research
Ho-Geun Kwak, Takehiro Suzuki, Naoshi Dohmae
Mass spectrometry (MS)-based characterization is important in proteomic research for verification of structural features and functional understanding of gene expression. Post-translational modifications (PTMs) such as methylation and acetylation have been reported to be associated with chromatin remodeling during spermatogenesis. Although antibody- and MS-based approaches have been applied for characterization of PTMs on H3 variants during spermatogenesis, variant-specific PTMs are still underexplored. We identified several lysine modifications in H3 variants, including testis-specific histone H3 (H3t), through their successful separation with MS-based strategy, based on differences in masses, retention times, and presence of immonium ions...
September 2017: Biochemistry and Biophysics Reports
Sabine A G Cuijpers, Edwin Willemstein, Alfred C O Vertegaal
Post translational protein modifications (PTMs) including small chemical groups and small proteins, belonging to the ubiquitin family, are essential for virtually all cellular processes. In addition to modification by a single PTM, proteins can be modified by a combination of different modifiers, which are able to influence each other. Since little is known about crosstalk between different ubiquitin family members, we developed an improved method enabling identification of co-modified proteins on a system-wide level using mass spectrometry...
September 26, 2017: Molecular & Cellular Proteomics: MCP
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