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https://www.readbyqxmd.com/read/28106519/subunit-mass-analysis-for-monitoring-antibody-oxidation
#1
Izabela Sokolowska, Jingjie Mo, Jia Dong, Michael J Lewis, Ping Hu
Methionine oxidation is a common posttranslational modification (PTM) of monoclonal antibodies (mAbs). Oxidation can reduce the in-vivo half-life, efficacy and stability of the product. Peptide mapping is commonly used to monitor the levels of oxidation, but this is a relatively time-consuming method. A high-throughput, automated subunit mass analysis method was developed to monitor antibody methionine oxidation. In this method, samples were treated with IdeS, EndoS and dithiothreitol to generate three individual IgG subunits (light chain, Fd' and single chain Fc)...
January 20, 2017: MAbs
https://www.readbyqxmd.com/read/28103160/yersinia-pestis-acetyltransferase-mediated-dual-acetylation-at-the-serine-and-lysine-residues-enhances-the-auto-ubiquitination-of-ubiquitin-ligase-march8-in-human-cells
#2
Cuiling Li, Daoguang Wang, Xin Lv, Ruirui Jing, Baibin Bi, Xinjun Chen, Jisheng Guo, Fengqin Wang, Shengnan Sun, Kazem M Azadzoi, Jing-Hua Yang
Lysine acetylation is known as a post translational modification (PTM) by histone acetyltransferases (HAT) that modifies histones and non-histone proteins to regulate gene expression. Serine acetylation, however, is reported in mammalian hosts by serine acetyltransferase of Yersinia pestis (YopJ) during infection. The protein target and cellular function of bacterial YopJ in mammalian systems are not fully addressed. Here we report dual acetylation at the serine and lysine residues by transiently expressed serine acetyltransferase YopJ mimicking Y...
January 19, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28078594/exploration-of-fas-s-nitrosylation-by-the-biotin-switch-assay
#3
Ali Bettaieb, Catherine Paul, Stéphanie Plenchette
S-nitrosylation is the covalent attachment of nitric oxide radical to the thiol side chain of cysteine. The death receptor Fas/CD95 can be S-nitrosylated in cancer cell lines by NO donors or iNOS activation. This posttranslational modification (PTM) induces Fas aggregation into lipid rafts and enhances FasL-mediated signaling and apoptosis. In this report, we describe the detection of Fas S-nitrosylation by the most commonly used method, the biotin switch assay (BSA) technique, that allows the detection of this very labile covalent modification in cells or tissues...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28072424/a-theoretical-and-experimental-investigation-of-mechanical-damage-to-rodent-sperm-generated-by-microscale-ice-formation
#4
X Han, J K Critser
:   BACKGROUND: Rodent sperm cryopreservation is of critical importance for the maintenance of lines or strains of genetically engineered mice and rats. However, rodent sperm are extremely mechanically sensitive due to their unusual morphology, and are severely damaged using current methods of cryopreservation. Those methods result in poor post thaw motility (PTM) for mouse. OBJECTIVE: To investigate the mechanism of mechanical damage introduced to rodent sperm during freezing, a micro-mechanical model was established to analyze the sperm radial and axial thermal stresses generated by microscale extracellular ice formation...
November 2016: Cryo Letters
https://www.readbyqxmd.com/read/28071717/tryptophan-and-non-tryptophan-fluorescence-of-the-eye-lens-proteins-provides-diagnostics-of-cataract-at-the-molecular-level
#5
Anna Gakamsky, Rory R Duncan, Nicola M Howarth, Baljean Dhillon, Kim K Buttenschön, Daniel J Daly, Dmitry Gakamsky
The chemical nature of the non-tryptophan (non-Trp) fluorescence of porcine and human eye lens proteins was identified by Mass Spectrometry (MS) and Fluorescence Steady-State and Lifetime spectroscopy as post-translational modifications (PTM) of Trp and Arg amino acid residues. Fluorescence intensity profiles measured along the optical axis of human eye lenses with age-related nuclear cataract showed increasing concentration of fluorescent PTM towards the lens centre in accord with the increased optical density in the lens nucleolus...
January 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28069893/alga-pras-algal-protein-annotation-suite-a-database-of-comprehensive-annotation-in-algal-proteomes
#6
Atsushi Kurotani, Yutaka Yamada, Tetsuya Sakurai
Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time, and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both, aquatic and terrestrial plants. In this study, we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algae and three plant species...
January 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28067524/urea-artifacts-interfere-with-immuno-purification-of-lysine-acetylation
#7
Ana Martinez-Val, Fernando Garcia, Pilar Ximénez-Embún, Ailyn Martínez Teresa-Calleja, Nuria Ibarz, Isabel Ruppen, Javier Munoz
Comprehensive analysis of post-translational modifications (PTMs) often depends on the purification of modified peptides prior to LC-MS/MS. The implementation of these enrichment methods requires thorough knowledge of the experimental conditions to achieve optimal selectivity and sensitivity. In this regard, large-scale analysis of lysine acetylation, a key PTM for multiple cellular processes, makes use of monoclonal pan-antibodies designed against this moiety. We report that the immuno-purification of lysine-acetylated peptides is hampered by the copurification of lysine carbamylated peptides, a frequent urea artifact...
January 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28059602/sumoylation-of-klf4-promotes-il-4-induced-macrophage-m2-polarization
#8
Kezhou Wang, Wei Zhou, Qi Cai, Jinke Cheng, Rong Cai, Rong Xing
Macrophages, in response to different environmental cues, undergo the classical polarization (M1 macrophages) as well as the alternative polarization (M2 macrophages) that involve the functions of stimulus-specific transcription factors. Kruppel-like factor 4 (KLF4), a member of a subfamily of the zinc-finger class of DNA-binding transcription factors, plays as a critical regulator of macrophage polarization. KLF4 has been reported as a SUMOylated protein. In this study, we showed that SUMOylation of KLF4, is induced by IL-4 treatment in macrophages...
January 6, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28043594/incidence-of-tuberculosis-among-children-living-in-contact-with-smear-positive-tuberculosis-advantages-and-limits-of-the-quantiferon-tb-gold-in-tube-test
#9
Djohar Hannoun, Fadila Boulahbal
OBJECTIVE/BACKGROUND: Children living in contact with smear-positive pulmonary tuberculosis (TB) patients are highly exposed to TB infection. Our objective was to estimate the incidence of TB in children living in contact with a Smear Positive (M+) pulmonary tuberculosis (PTM+) index case during 2years following exposure. METHODS: This was a descriptive, cohort, prospective, multicenter study of children aged from 6months to 15years in contact with a PTM+ case. The recruitment of children has been based on the diagnosed PTM+ index case and taken in charge by the Services of Control of Tuberculosis and Respiratory Diseases located in Algiers during 2014...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28043171/the-story-of-protein-arginine-methylation-characterization-regulation-and-function
#10
Chao Peng, Catherine Cl Wong
Arginine methylation is an important post-translational modification (PTM) in cells, which is catalyzed by a group of protein arginine methyltransferases (PRMTs). It plays significant roles in diverse cellular processes and various diseases. Misregulation and aberrant expression of PRMTs can provide potential biomarkers and therapeutic targets for drug discovery. Areas covered: Herein, we review the arginine methylation literature and summarize the methodologies for the characterization of this modification, as well as describe the recent insights into arginine methyltransferases and their biological functions in diseases...
February 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28040940/pressure-calibration-in-solid-pressure-transmitting-medium-in-large-volume-press
#11
Xiaozhi Yan, Xiangting Ren, Duanwei He
The pressure limit in the large-volume-press (LVP) is increasing, but the in situ pressure calibration in LVP is still not a well resolved problem. The variation of the electrical resistance of the manganin with pressure in a hydrostatic condition is well known and is widely used in the pressure calibration in LVP. However, the hydrostatic pressure condition is hard to be maintained for the unavoidable solidification of the pressure transmitting medium (PTM) with pressure increasing. Moreover, our understanding about the relationship between pressure and manganin's resistance in a solid transmitting medium is still limited...
December 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28034318/sensitive-and-precise-characterization-of-combinatorial-histone-modifications-by-selective-derivatization-coupled-with-rplc-ethcd-ms-ms
#12
Rijing Liao, Dan Zheng, Aiying Nie, Shaolian Zhou, Haibing Deng, Yuan Gao, Pengyuan Yang, Yanyan Yu, Lin Tan, Wei Qi, Jiaxi Wu, En Li, Wei Yi
Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography-mass spectrometry approaches for online separation of variously modified histone peptides. Here we provide a novel strategy that combines the selective histone peptide derivatization using N-hydroxysuccinimide propionate ester with reversed-phase liquid chromatography (RPLC) for the robust, sensitive, and reliable characterization of combinatorial histone PTMs...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28031468/prmt5-c-terminal-phosphorylation-modulates-a-14-3-3-pdz-interaction-switch
#13
Alexsandra B Espejo, Guozhen Gao, Karynne Black, Sitaram Gayatri, Nicolas Veland, Jeesun Kim, Taiping Chen, Marius Sudol, Cheryl Walker, Mark T Bedford
PRMT5 is the primary enzyme responsible for the deposition of the symmetric dimethylarginine in mammalian cells. In an effort to understand how PRMT5 is regulated we identified a threonine phosphorylation site within a C-terminal tail motif, which is targeted by the AKT/SGK kinases. While investigating the function of this posttranslational modification (PTM) we serendipitously discovered that its free C-terminal tail binds PDZ domains (when unphosphorylated) and 14-3-3 proteins (when phosphorylated). In essence, a phosphorylation event within the last few residues of the C-terminal tail generates a PTM-dependent PDZ/14-3-3 interaction switch...
December 28, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28025199/computational-prediction-of-species-specific-malonylation-sites-via-enhanced-characteristic-strategy
#14
Li-Na Wang, Shao-Ping Shi, Hao-Dong Xu, Ping-Ping Wen, Jian-Ding Qiu
MOTIVATION: Protein malonylation is a novel post-translational modification (PTM) which orchestrates a variety of biological processes. Annotation of malonylation in proteomics is the first-crucial step to decipher its physiological roles which are implicated in the pathological processes. Comparing with the expensive and laborious experimental research, computational prediction can provide an accurate and effective approach to the identification of many types of PTMs sites. However, there is still no online predictor for lysine malonylation...
December 23, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28011818/the-emerging-complexity-of-ubiquitin-architecture
#15
Fumiaki Ohtake, Hikaru Tsuchiya
Ubiquitylation is an essential post-translational modification (PTM) of proteins with diverse cellular functions. Polyubiquitin chains with different topologies have different cellular roles, and are referred to as a 'ubiquitin code'. Recent studies have begun to reveal that more complex ubiquitin architectures function as important signals in several biological pathways. These include PTMs of ubiquitin itself, such as acetylated ubiquitin and phospho-ubiquitin. Moreover, important roles for heterogeneous polyubiquitin chains, such as mixed or branched chains, have been reported, which significantly increase the diversity of the ubiquitin code...
December 23, 2016: Journal of Biochemistry
https://www.readbyqxmd.com/read/28004786/gps-pail-prediction-of-lysine-acetyltransferase-specific-modification-sites-from-protein-sequences
#16
Wankun Deng, Chenwei Wang, Ying Zhang, Yang Xu, Shuang Zhang, Zexian Liu, Yu Xue
Protein acetylation catalyzed by specific histone acetyltransferases (HATs) is an essential post-translational modification (PTM) and involved in the regulation a broad spectrum of biological processes in eukaryotes. Although several ten thousands of acetylation sites have been experimentally identified, the upstream HATs for most of the sites are unclear. Thus, the identification of HAT-specific acetylation sites is fundamental for understanding the regulatory mechanisms of protein acetylation. In this work, we first collected 702 known HAT-specific acetylation sites of 205 proteins from the literature and public data resources, and a motif-based analysis demonstrated that different types of HATs exhibit similar but considerably distinct sequence preferences for substrate recognition...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28003186/posttranslational-modifications-of-tubulin-and-cilia
#17
Dorota Wloga, Ewa Joachimiak, Panagiota Louka, Jacek Gaertig
Tubulin undergoes several highly conserved posttranslational modifications (PTMs) including acetylation, detyrosination, glutamylation, and glycylation. These PTMs accumulate on a subset of microtubules that are long-lived, including those in the basal bodies and axonemes. Tubulin PTMs are distributed nonuniformly. In the outer doublet microtubules of the axoneme, the B-tubules are highly enriched in the detyrosinated, polyglutamylated, and polyglycylated tubulin, whereas the A-tubules contain mostly unmodified tubulin...
December 21, 2016: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28002468/conserved-lysine-acetylation-within-the-microtubule-binding-domain-regulates-map2-tau-family-members
#18
Andrew W Hwang, Hanna Trzeciakiewicz, Dave Friedmann, Chao-Xing Yuan, Ronen Marmorstein, Virginia M Y Lee, Todd J Cohen
Lysine acetylation has emerged as a dominant post-translational modification (PTM) regulating tau proteins in Alzheimer's disease (AD) and related tauopathies. Mass spectrometry studies indicate that tau acetylation sites cluster within the microtubule-binding region (MTBR), a region that is highly conserved among tau, MAP2, and MAP4 family members, implying that acetylation could represent a conserved regulatory mechanism for MAPs beyond tau. Here, we combined mass spectrometry, biochemical assays, and cell-based approaches to demonstrate that the tau family members MAP2 and MAP4 are also subject to reversible acetylation...
2016: PloS One
https://www.readbyqxmd.com/read/27997253/the-progress-and-potential-of-proteomic-biomarkers-for-type-1-diabetes-in-children
#19
Robert Moulder, Santosh Dilip Bhosale, Riitta Lahesmaa, David Robinson Goodlett
Although it is possible to identify the genetic risk for type 1 diabetes (T1D), it is not possible to predict who will develop the disease. New biomarkers are needed that would help understand the mechanisms of disease onset and when to administer targeted therapies and interventions. Areas covered: An overview is presented of international study efforts towards understanding the cause of T1D, including the collection of several extensive temporal sample series that follow the development of T1D in at risk children...
January 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27994639/interpreting-comprehensive-two-dimensional-gas-chromatography-using-peak-topography-maps-with-application-to-petroleum-forensics
#20
Hamidreza Ghasemi Damavandi, Ananya Sen Gupta, Robert K Nelson, Christopher M Reddy
BACKGROUND: Comprehensive two-dimensional gas chromatography [Formula: see text] provides high-resolution separations across hundreds of compounds in a complex mixture, thus unlocking unprecedented information for intricate quantitative interpretation. We exploit this compound diversity across the [Formula: see text] topography to provide quantitative compound-cognizant interpretation beyond target compound analysis with petroleum forensics as a practical application. We focus on the [Formula: see text] topography of biomarker hydrocarbons, hopanes and steranes, as they are generally recalcitrant to weathering...
2016: Chemistry Central Journal
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