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Jing Liu, Bo Xu, Zheyi Liu, Mingming Dong, Jiawei Mao, Ye Zhou, Jin Chen, Fangjun Wang, Hanfa Zou
Mass spectrometry (MS) based quantitative analyses of proteome and proteome post-translational modifications (PTMs) play more and more important roles in biological, pharmaceutical and clinical studies. However, it is still a big challenge to accurately quantify the proteins or proteins PTM sites with extreme relative abundances in comparative protein samples, such as the significantly dysregulated ones. Herein, a novel quantification strategy, Mixing at Specific Ratio (MaSR) before isotope labeling, had been developed to improve the quantification accuracy and coverage of extreme proteins and protein phosphorylation sites...
January 15, 2017: Analytica Chimica Acta
Kristína Durdíková, Miroslav Chovanec
DNA double-strand breaks are the most serious type of DNA damage and non-homologous end joining (NHEJ) is an important pathway for their repair. In Saccharomyces cerevisiae, three complexes mediate the canonical NHEJ pathway, Ku (Ku70/Ku80), MRX (Mre11/Rad50/Xrs2) and DNA ligase IV (Dnl4/Lif1). Mammalian NHEJ is more complex, primarily as a consequence of the fact that more factors are involved in the process, and also because higher chromatin organization and more complex regulatory networks exist in mammals...
December 3, 2016: Current Genetics
Yan Xu, Ya-Xin Ding, Jun Ding, Ling-Yun Wu, Yu Xue
Lysine malonylation is an important post-translational modification (PTM) in proteins, and has been characterized to be associated with diseases. However, identifying malonyllysine sites still remains to be a great challenge due to the labor-intensive and time-consuming experiments. In view of this situation, the establishment of a useful computational method and the development of an efficient predictor are highly desired. In this study, a predictor Mal-Lys which incorporated residue sequence order information, position-specific amino acid propensity and physicochemical properties was proposed...
December 2, 2016: Scientific Reports
Capilla Mata-Pérez, Juan C Begara-Morales, Mounira Chaki, Beatriz Sánchez-Calvo, Raquel Valderrama, María N Padilla, Francisco J Corpas, Juan B Barroso
In recent years, the study of nitric oxide (NO) in plant systems has attracted the attention of many researchers. A growing number of investigations have shown the significance of NO as a signal molecule or as a molecule involved in the response against (a)biotic processes. NO can be responsible of the post-translational modifications (NO-PTM) of target proteins by mechanisms such as the nitration of tyrosine residues. The study of protein tyrosine nitration during development and under biotic and adverse environmental conditions has increased in the last decade; nevertheless, there is also an endogenous nitration which seems to have regulatory functions...
2016: Frontiers in Plant Science
Paulo André Dias Bastos, João Pinto da Costa, Rui Vitorino
Protein post-translational modifications (PTMs) are a key bacterial feature that holds the capability to modulate protein function and responses to environmental cues. Until recently, their role in the regulation of prokaryotic systems has been largely neglected. However, the latest developments in mass spectrometry-based proteomics have allowed an unparalleled identification and quantification of proteins and peptides that undergo PTMs in bacteria, including in species which directly or indirectly affect human health...
November 23, 2016: Journal of Proteomics
Danxi Zhu, Lidan Hou, Bin Hu, Hang Zhao, Jie Sun, Jianhua Wang, Xiangjun Meng
Protein lysine acetylation and succinylation play important regulatory roles in cells, both of which or each other has a close relationship. Dichloroacetate (DCA), a well-known pyruvate dehydrogenase kinase (PDK) inhibitor, has the potential to be used as anti-cancer drugs for several tumors including colorectal cancer. However, little is known about the potential mechanism of DCA-based cancer therapy by protein posttranslational modifications (PTM) including global proteome, acetylome and succinylome. Here the combinations with stable isotope labeling (SILAC), antibody affinity enrichment and high resolution LC-MS/MS analysis were performed in human colon cancer HCT116 cells...
November 22, 2016: Scientific Reports
Jeffrey D Rudolf, Liao-Bin Dong, Ben Shen
Natural products have served as the main source of drugs and drug leads, and natural products produced by microorganisms are one of the most prevalent sources of clinical antibiotics. Their unparalleled structural and chemical diversities provide a basis to investigate fundamental biological processes while providing access to a tremendous amount of chemical space. There is a pressing need for novel antibiotics with new mode of actions to combat the growing challenge of multidrug resistant pathogens. This review begins with the pioneering discovery and biological activities of platensimycin (PTM) and platencin (PTN), two antibacterial natural products isolated from Streptomyces platensis...
November 16, 2016: Biochemical Pharmacology
Gonca Seber, Alexander Rudnev, Andrea Droghetti, Ivan Rungger, Jaume Veciana, Marta Mas-Torrent, Concepció Rovira, Núria Crivillers
A novel, persistent, electrochemically active perchlorinatedtriphenylmethyl (PTM) radical with a diazonium functionality has been covalently attached onto highly ordered pyrolytic graphite by electrografting in a single-step process. Electrochemical scanning tunneling microscopy (EC-STM) and Raman spectrocopy measurements revealed that PTM molecules have a higher tendency to covalently react at the HOPG step edges. The cross-section profiles from EC-STM images showed that there is current enhancement at the functionalized areas, which can be explained by redox mediated electron tunneling through surface-confined redox-active molecules...
November 18, 2016: Chemistry: a European Journal
Alessandro Cuomo, Monica Soldi, Tiziana Bonaldi
Histone posttranslational modifications (hPTMs) play a key role in regulating chromatin dynamics and fine-tuning DNA-based processes. Mass spectrometry (MS) has emerged as a versatile technology for the analysis of histones, contributing to the dissection of hPTMs, with special strength in the identification of novel marks and in the assessment of modification cross talks. Stable isotope labeling by amino acid in cell culture (SILAC), when adapted to histones, permits the accurate quantification of PTM changes among distinct functional states; however, its application has been mainly confined to actively dividing cell lines...
2017: Methods in Molecular Biology
Aleem Syed, Neha Arora, Thomas A Bunch, Emily A Smith
Cysteine residues (Cys) in the membrane proximal region are common post-translational modification (PTM) sites in transmembrane proteins. Herein, the effects of a highly conserved membrane proximal α-subunit Cys(1368) on the diffusion properties of αPS2CβPS integrins are reported. Sequence alignment shows that this cysteine is palmitoylated in human α3 and α6 integrin subunits. Replacing Cys(1368) in wild-type integrins with valine (Val(1368)) putatively blocks a PTM site and alters integrins' ligand binding and diffusion characteristics...
November 15, 2016: Physical Biology
Ilirian Dhimitruka, Yasmin Alsayed Alzarie, Craig Hemann, Alexandre Samouilov, Jay L Zweier
EPR oximetry with the use of trityl radicals can enable sensitive O2 measurement in biological cells and tissues. However, in vitro cellular and in vivo biological applications are limited by rapid trityl probe degradation or biological clearance and the need to enhance probe O2 sensitivity. We synthesized novel perfluorocarbon (PFC) emulsions, ∼200nm droplet size, containing esterified perchlorinated triphenyl methyl (PTM) radicals dispersed in physiological aqueous buffers. These formulations exhibit excellent EPR signal stability, over 20-fold greater than free PTM probes, with high oxygen sensitivity ∼17mG/mmHg enabling pO2 measurement in aqueous solutions or cell suspensions with sensitivity >0...
October 24, 2016: Bioorganic & Medicinal Chemistry Letters
Raja Rajeswary Thanmalagan, Leimarembi Devi Naorem, Amouda Venkatesan
Breast cancer affects every 1 of 3000 pregnant women or in the first post-partum year is referred as Pregnancy Associated Breast Cancer (PABC) in mid 30s. Even-though rare disease, classified under hormone receptor negative status which metastasis quickly to other parts by extra cellular matrix degradation. Hence it is important to find an optimal treatment option for a PABC patient. Also additional care should be taken to choose the drug; in order to avoid fetal malformation and post-partum stage side-effects...
November 10, 2016: Pathology Oncology Research: POR
Jianhang Guo, Juanxu Liu, Qian Wei, Rongmin Wang, Weiyuan Yang, Yueyue Ma, Guoju Chen, Yuyixun Yu
Petal senescence is a complex programmed process. It has been previously demonstrated that treatment with ethylene, a plant hormone involved in senescence, can extensively alter transcriptome and proteome profiles in plants. However, little is known regarding the impact of ethylene on post-translational modification (PTM) or the association between PTM and the proteome. Protein degradation is one of the hallmarks of senescence, and ubiquitination, a major PTM in eukaryotes, plays important roles in protein degradation...
November 3, 2016: Plant Physiology
Sara P Culleton, Sriramana Kanginakudru, Marsha DeSmet, Timra Gilson, Fang Xie, Shwu-Yuan Wu, Cheng-Ming Chiang, Guihong Qi, Mu Wang, Elliot J Androphy
: Papillomaviruses are small, double-stranded DNA viruses that encode the E2 protein, which controls transcription, replication, and genome maintenance in infected cells. Post-translational modifications (PTM) affecting E2 function and stability have been demonstrated for multiple types of papillomaviruses. Here we describe the first phosphorylation event of a conserved tyrosine (Y) in the bovine papillomavirus type 1 (BPV-1) E2 protein at amino acid 102. While its phospho-deficient mutant phenylalanine (F) activated both transcription and replication in luciferase reporter assays, the mutant that may act as a phospho-mimetic, Y102 to glutamate (E), lost both activities...
November 2, 2016: Journal of Virology
Francisco Simões, Maria Manuela Calheiros
The main goal of this study is to understand the relationship between different types of prosocial behaviors and different forms of self-regulation, as part of the adaptation and validation of the Portuguese version of the Prosocial Tendencies Measure-Revised (PTM-R). A total of 403 early adolescents (M = 11.81; SD = .92; 52.91% girls) completed self-reported measures. The evaluation of psychometric properties of the PTM-R involved a confirmatory factorial analysis, followed by the examination of factorial internal consistency and factorial invariance analyses across gender groups and school retention groups (retention vs...
November 3, 2016: Spanish Journal of Psychology
Paula Korkuć, Dirk Walther
Post-translational modifications (PTMs) represent an important regulatory layer influencing the structure and function of proteins. With broader availability of experimental information on the occurrences of different PTM types, the investigation of a potential "crosstalk" between different PTM types and combinatorial effects have moved into the research focus. Hypothesizing that relevant interferences between different PTM types and sites may become apparent when investigating their mutual physical distances, we performed a systematic survey of pairwise homo- and heterotypic distances of seven frequent PTM types considering their sequence and spatial distances in resolved protein structures...
November 1, 2016: Proteins
Hao Hu, Xi Gu, Liang-Jiao Xue, Prashant S Swamy, Scott A Harding, Chung-Jui Tsai
Cortical microtubules (MTs) are evolutionarily conserved cytoskeletal components with specialized roles in plants, including regulation of cell wall biogenesis. MT functions and dynamics are dictated by the composition of their monomeric subunits, α- (TUA) and β-tubulins (TUB), which in animals and protists are subject to both transcriptional regulation and post-translational modifications (PTM). While spatiotemporal regulation of tubulin gene expression has been reported in plants, whether and to what extent tubulin PTMs occur in these species remain poorly understood...
2016: Frontiers in Plant Science
Aparna Rao, Debananda Padhy, Sarada Sarangi, Gopinath Das
PURPOSE: To evaluate the angle closure scoring system (ACSS) for stratifying primary angle course disease. METHODS: This observational cross sectional institutional study included patients with primary open angle glaucoma suspects (n = 21) and primary angle closure disease (primary angle closure, PAC, n = 63 and primary angle course glaucoma, PACG, n = 58 (defined by International society of Geographical and Epidemiological Ophthalmology, ISGEO). Two independent examiners blinded to clinical details, graded good quality pre-laser goniophotographs of the patients incorporating quadrants of peripheral anterior synechieae (PAS), non-visibility of posterior trabecular meshwork (PTM) and blotchy pigments (ranging from 1-4 quadrants), iris configuration, angle recess (sum of above depicting ACSSg) and lens thickness/axial length ratio (LT/AL), cup disc ratio and baseline intraocular pressure (IOP) to give total score (ACSSt)...
2016: PloS One
Marcin Tatjewski, Marcin Kierczak, Dariusz Plewczynski
Here, we present two perspectives on the task of predicting post translational modifications (PTMs) from local sequence fragments using machine learning algorithms. The first is the description of the fundamental steps required to construct a PTM predictor from the very beginning. These steps include data gathering, feature extraction, or machine-learning classifier selection. The second part of our work contains the detailed discussion of more advanced problems which are encountered in PTM prediction task...
2017: Methods in Molecular Biology
Yue Zhang, Shiaw-Lin Wu, Yinyin Li
Capture reagents are critical to affinity-based bioanalytical methods. The potential bias of capture reagents, for or against certain subpopulations of the target of interest, may lead to inaccurate quantitation. This issue is more profound for sensitive measurements, such as post-translational modification (PTM) profiling of therapeutic proteins from complex matrix. Here, a recently developed affinity purification coupled mass spectrometric method was utilized to assess the full sequence of a circulating therapeutic aglycosylated IgG1 (MAB3) in human subject, using two different capture reagents...
October 21, 2016: Biologicals: Journal of the International Association of Biological Standardization
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