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https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#1
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28218834/unambiguous-identification-of-serine-and-threonine-pyrophosphorylation-using-neutral-loss-triggered-ethcd-mass-spectrometry
#2
Martin Penkert, Lisa M Yates, Michael Schuemann, David H Perlman, Dorothea Fiedler, Eberhard Krause
Tandem mass spectrometry (MS/MS) has emerged as the core technology for identification of posttranslational modifications (PTMs). Here, we report the mass spectrometry analysis of serine and threonine pyrophosphorylation, a protein modification that has eluded detection by conventional MS/MS methods. Analysis of a set of synthesized, site-specifically modified peptides by different fragmentation techniques shows that pyrophosphorylated peptides exhibit a characteristic neutral loss pattern of 98, 178 and 196 Da, which enables the distinction between isobaric pyro- and diphosphorylated peptides...
February 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28209382/err%C3%AE-a-junior-orphan-with-a-senior-role-in-metabolism
#3
REVIEW
Jagannath Misra, Don-Kyu Kim, Hueng-Sik Choi
Estrogen-related receptor (ERR)γ is an orphan nuclear hormone receptor that belongs to the ERR subfamily of transcription factors. No endogenous ligand has been identified to date. ERRγ possesses ligand-independent transcriptional activity that is regulated by co-regulator interactions, and post-translational modifications (PTMs). Recent data from animal models have established ERRγ as a crucial mediator of multiple endocrine and metabolic signals. ERRγ plays important roles in pathological conditions such as insulin resistance, alcoholic liver injury, and cardiac hypertrophy, and controls energy metabolism in the heart, skeletal muscle, and pancreatic β cells...
February 13, 2017: Trends in Endocrinology and Metabolism: TEM
https://www.readbyqxmd.com/read/28209140/papillary-thyroid-microcarcinoma-the-significance-of-high-risk-features
#4
Nori L Bradley, Sam M Wiseman
BACKGROUND: Papillary carcinomas that measure 1.0cm or less are diagnosed as papillary thyroid microcarcinomas (PTMs). The clinical significance and recommendations for management of these PTMs is still evolving. The objective of the study was to compare the characteristics of small (<5mm) to large (≥ 5mm) papillary thyroid microcarcinomas. METHODS: Amongst 1459 sequential patients undergoing thyroid surgery at a single center, 132 (9%) cases were diagnosed with PTM...
February 16, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28199195/tissue-transglutaminase-tg2-and-mitochondrial-function-and-dysfunction
#5
Thung-S Lai, Cheng-Jui Lin, Yu-Ting Wu, Chih-Jen Wu
Mitochondria are the cell's power plant to satisfy the energy demands. However, dysfunctional mitochondria can cause overproduction of reactive oxygen species (ROS), oxidative stress, and alteration of calcium homeostasis, which are the hallmarks of mitochondrial diseases. Under prolong oxidative stress, repeated cytosolic calcium elevations even only transiently, can lead to activation of some enzymes. One calcium-activated enzyme with demonstrated pathophysiological important in mitochondrial disease is tissue transglutaminase (TG2)...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28199194/regulation-of-mitochondrial-gene-expression-the-epigenetic-enigma
#6
Archibold Mposhi, Monique Gp Van der Wijst, Klaas Nico Faber, Marianne G Rots
Epigenetics provides an important layer of information on top of the DNA sequence and is essential for establishing gene expression profiles. Extensive studies have shown that nuclear DNA methylation and histone modifications influence nuclear gene expression. However, it remains unclear whether mitochondrial DNA (mtDNA) undergoes similar epigenetic changes to regulate mitochondrial gene expression. Recently, it has been shown that mtDNA is differentially methylated in various diseases such as diabetes and colorectal cancer...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28197170/glutathionylation-of-pea-chloroplast-2-cys-prx-and-mitochondrial-prx-iif-affects-their-structure-and-peroxidase-activity-and-sulfiredoxin-deglutathionylates-only-the-2-cys-prx
#7
Aingeru Calderón, Alfonso Lázaro-Payo, Iván Iglesias-Baena, Daymi Camejo, Juan J Lázaro, Francisca Sevilla, Ana Jiménez
Together with thioredoxins (Trxs), plant peroxiredoxins (Prxs), and sulfiredoxins (Srxs) are involved in antioxidant defense and redox signaling, while their regulation by post-translational modifications (PTMs) is increasingly regarded as a key component for the transduction of the bioactivity of reactive oxygen and nitrogen species. Among these PTMs, S-glutathionylation is considered a protective mechanism against overoxidation, it also modulates protein activity and allows signaling. This study explores the glutathionylation of recombinant chloroplastic 2-Cys Prx and mitochondrial Prx IIF from Pisum sativum...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28194967/multicellular-tumor-spheroids-combined-with-mass-spectrometric-histone-analysis-to-evaluate-epigenetic-drugs
#8
Peter E Feist, Simone Sidoli, Xin Liu, Monica M Schroll, Sharif Rahmy, Rina Fujiwara, Benjamin A Garcia, Amanda B Hummon
Multicellular tumor spheroids (MCTS) are valuable in vitro tumor models frequently used to evaluate the penetration and efficacy of therapeutics. In this study, we evaluated potential differences in epigenetic markers, i.e., histone post-translational modifications (PTMs), in the layers of the HCT116 colon carcinoma MCTS. Cells were grown in agarose-coated 96 well plates, forming reproducible 1-mm-diameter MCTS. The MCTS were fractionated into three radially concentric portions, generating samples containing cells from the core, the mid and the external layers...
February 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28179408/time-resolved-global-and-chromatin-proteomics-during-herpes-simplex-virus-hsv-1-infection
#9
Katarzyna Kulej, Daphne C Avgousti, Simone Sidoli, Christin Herrmann, Ashley N Della Fera, Eui Tae Kim, Benjamin A Garcia, Matthew D Weitzman
Herpes simplex virus (HSV-1) lytic infection results in global changes to the host cell proteome and the proteins associated with host chromatin. We present a system level characterization of proteome dynamics during infection by performing a multi-dimensional analysis during HSV-1 lytic infection of human foreskin fibroblast (HFF) cells. Our study includes identification and quantification of the host and viral proteomes, phosphoproteomes, chromatin bound proteomes and post-translational modifications (PTMs) on cellular histones during infection...
February 8, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28177766/functional-assessment-of-mecp2-in-rett-syndrome-and-cancers-of-breast-colon-and-prostate
#10
Somnath Pandey, Kevin Pruitt
Ever since the first report that mutations in methyl-CpG-binding protein 2 (MeCP2) causes Rett syndrome (RTT), a severe neurological disorder in females world-wide, there has been a keen interest to gain a comprehensive understanding of this protein. While the classical model associated with MeCP2 function suggests its role in gene suppression via recruitment of co-repressor complexes and histone deacetylases to methylated CpG-sites, recent discoveries have brought to light its role in transcription activation, modulation of RNA splicing and chromatin compaction...
November 10, 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28174683/post-translational-modifications-of-annexin-a2-are-linked-to-its-association-with-perinuclear-nonpolysomal-mrnp-complexes
#11
Ingvild Aukrust, Linn Andersen Rosenberg, Mia Madeleine Ankerud, Vibeke Bertelsen, Hanne Hollås, Jaakko Saraste, Ann Kari Grindheim, Anni Vedeler
Various post-translational modifications (PTMs) regulate the localisation and function of the multifunctional protein Annexin A2 (AnxA2). In addition to its various tasks as a cytoskeletal- and membrane-associated protein, AnxA2 can function as a trans-acting protein binding to cis-acting sequences of specific mRNAs. In the present study, we have examined the role of Ser25 phosphorylation in subcellular localisation of AnxA2 and its interaction with mRNP complexes. Subcellular fractionation and confocal microscopy of rat neuroendocrine PC12 cells showed that Ser25-phosphorylated AnxA2 (pSer25AnxA2) is absent from the nucleus and mainly localised to the perinuclear region, evidently associating with both membranes and cytoskeletal elements...
February 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28152592/flagging-false-positives-following-untargeted-lc-ms-characterization-of-histone-post-translational-modification-combinations
#12
Sander Willems, Maarten Dhaenens, Elisabeth Govaert, Laura De Clerck, Paulien Meert, Christophe Van Neste, Filip Van Nieuwerburgh, Dieter Deforce
Epigenetic changes can be studied with an untargeted characterization of histone post-translational modifications (PTMs) by liquid chromatography-mass spectrometry (LC-MS). While prior information about more than 20 types of histone PTMs exists, little is known about histone PTM combinations (PTMCs). Because of the combinatorial explosion it is intrinsically impossible to consider all potential PTMCs in a database search. Consequentially, high-scoring false positives with unconsidered but correct alternative isobaric PTMCs can occur...
February 3, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28150252/cross-species-ptm-mapping-from-phosphoproteomic-data
#13
Rima Chaudhuri, Jean Yee Hwa Yang
Protein post-translational modifications (PTMs) are crucial for signal transduction in cells. In order to understand key cell signaling events, identification of functionally important PTMs, which are more likely to be evolutionarily conserved, is necessary. In recent times, high-throughput mass spectrometry (MS) has made quantitative datasets in diverse species readily available, which has led to a growing need for tools to facilitate cross-species comparison of PTM data. Cross-species comparison of PTM sites is difficult since they often lie in structurally disordered protein domains...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150251/computational-and-statistical-methods-for-high-throughput-mass-spectrometry-based-ptm-analysis
#14
Veit Schwämmle, Marc Vaudel
Cell signaling and functions heavily rely on post-translational modifications (PTMs) of proteins. Their high-throughput characterization is thus of utmost interest for multiple biological and medical investigations. In combination with efficient enrichment methods, peptide mass spectrometry analysis allows the quantitative comparison of thousands of modified peptides over different conditions. However, the large and complex datasets produced pose multiple data interpretation challenges, ranging from spectral interpretation to statistical and multivariate analyses...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150246/iptmnet-integrative-bioinformatics-for-studying-ptm-networks
#15
Karen E Ross, Hongzhan Huang, Jia Ren, Cecilia N Arighi, Gang Li, Catalina O Tudor, Mengxi Lv, Jung-Youn Lee, Sheng-Chih Chen, K Vijay-Shanker, Cathy H Wu
Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for user-friendly bioinformatics resources that capture PTM information from the literature and support analyses of PTMs and their functional consequences. This chapter describes the use of iPTMnet ( http://proteininformationresource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150245/bioinformatics-analysis-of-ptm-modified-protein-interaction-networks-and-complexes
#16
Jonathan Woodsmith, Ulrich Stelzl, Arunachalam Vinayagam
Normal cellular functioning is maintained by macromolecular machines that control both core and specialized molecular tasks. These machines are in large part multi-subunit protein complexes that undergo regulation at multiple levels, from expression of requisite components to a vast array of post-translational modifications (PTMs). PTMs such as phosphorylation, ubiquitination, and acetylation currently number more than 200,000 in the human proteome and function within all molecular pathways. Here we provide a framework for systematically studying these PTMs in the context of global protein-protein interaction networks...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150244/bioinformatics-analysis-of-functional-associations-of-ptms
#17
Pablo Minguez, Peer Bork
Post-translational modifications (PTMs) are an important source of protein regulation; they fine-tune the function, localization, and interaction with other molecules of the majority of proteins and are partially responsible for their multifunctionality. Usually, proteins have several potential modification sites, and their patterns of occupancy are associated with certain functional states. These patterns imply cross talk among PTMs within and between proteins, the majority of which are still to be discovered...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150240/analysis-of-protein-phosphorylation-and-its-functional-impact-on-protein-protein-interactions-via-text-mining-of-the-scientific-literature
#18
Qinghua Wang, Karen E Ross, Hongzhan Huang, Jia Ren, Gang Li, K Vijay-Shanker, Cathy H Wu, Cecilia N Arighi
Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein phosphorylation represents an essential regulatory mechanism that plays a role in many biological processes. Protein kinases, the enzymes catalyzing this reaction, are key participants in metabolic and signaling pathways. Their activation or inactivation dictate downstream events: what substrates are modified and their subsequent impact (e.g., activation state, localization, protein-protein interactions (PPIs))...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150239/analysis-of-cysteine-redox-post-translational-modifications-in-cell-biology-and-drug-pharmacology
#19
Revati Wani, Brion W Murray
Reversible cysteine oxidation is an emerging class of protein post-translational modification (PTM) that regulates catalytic activity, modulates conformation, impacts protein-protein interactions, and affects subcellular trafficking of numerous proteins. Redox PTMs encompass a broad array of cysteine oxidation reactions with different half-lives, topographies, and reactivities such as S-glutathionylation and sulfoxidation. Recent studies from our group underscore the lesser known effect of redox protein modifications on drug binding...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28150238/impact-of-nonsynonymous-single-nucleotide-variations-on-post-translational-modification-sites-in-human-proteins
#20
Naila Gulzar, Hayley Dingerdissen, Cheng Yan, Raja Mazumder
Post-translational modifications (PTMs) are covalent modifications that proteins might undergo following or sometimes during the process of translation. Together with gene diversity, PTMs contribute to the overall variety of possible protein function for a given organism. Single-nucleotide polymorphisms (SNPs) are the most common form of variations found in the human genome, and have been found to be associated with diseases like Alzheimer's disease (AD) and Parkinson's disease (PD), among many others. Studies have also shown that non-synonymous single-nucleotide variation (nsSNV) at the PTM site, which alters the corresponding encoded amino acid in the translated protein sequence, can lead to abnormal activity of a protein and can contribute to a disease phenotype...
2017: Methods in Molecular Biology
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