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PTM cross-talk

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https://www.readbyqxmd.com/read/28683815/metabolic-labeling-in-middle-down-proteomics-allows-for-investigation-of-the-dynamics-of-the-histone-code
#1
Simone Sidoli, Congcong Lu, Mariel Coradin, Xiaoshi Wang, Kelly R Karch, Chrystian Ruminowicz, Benjamin A Garcia
BACKGROUND: Middle-down mass spectrometry (MS), i.e., analysis of long (~50-60 aa) polypeptides, has become the method with the highest throughput and accuracy for the characterization of combinatorial histone posttranslational modifications (PTMs). The discovery of histone readers with multiple domains, and overall the cross talk of PTMs that decorate histone proteins, has revealed that histone marks have synergistic roles in modulating enzyme recruitment and subsequent chromatin activities...
July 6, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28459814/co-occurring-protein-phosphorylation-are-functionally-associated
#2
Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li
Post-translational modifications (PTMs) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions. With the increasing number of known PTM sites, it becomes imperative to understand their functional interplays. In this study, we proposed a novel analytical strategy to explore functional relationships between PTM sites by testing their tendency to be modified together (co-occurrence) under the same condition, and applied it to proteome-wide human phosphorylation data collected under 88 different laboratory or physiological conditions...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28447979/reconstitution-of-nucleosomes-with-differentially-isotope-labeled-sister-histones
#3
Stamatios Liokatis
Asymmetrically modified nucleosomes contain the two copies of a histone (sister histones) decorated with distinct sets of Post-translational Modifications (PTMs). They are newly identified species with unknown means of establishment and functional implications. Current analytical methods are inadequate to detect the copy-specific occurrence of PTMs on the nucleosomal sister histones. This protocol presents a biochemical method for the in vitro reconstitution of nucleosomes containing differentially isotope-labeled sister histones...
March 26, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27854018/silac-based-quantitative-strategies-for-accurate-histone-posttranslational-modification-profiling-across-multiple-biological-samples
#4
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
https://www.readbyqxmd.com/read/27619687/vegf-a-vegfr2-signaling-network-in-endothelial-cells-relevant-to-angiogenesis
#5
Chandran S Abhinand, Rajesh Raju, Sasikumar J Soumya, Prabha S Arya, Perumana R Sudhakaran
Vascular endothelial growth factor-A (VEGF-A) is essential for endothelial cell functions associated with angiogenesis. Signal transduction networks initiated by VEGFA/VEGFR2, the most prominent ligand-receptor complex in the VEGF system, leads to endothelial cell proliferation, migration, survival and new vessel formation involved in angiogenesis. Considering its biomedical importance, we have developed the first comprehensive map of endothelial cell-specific signaling events of VEGFA/VEGFR2 system pertaining to angiogenesis...
December 2016: Journal of Cell Communication and Signaling
https://www.readbyqxmd.com/read/27618775/prediction-of-post-translation-modifications-at-the-contact-site-between-anaplasma-phagocytophilum-and-human-host-during-autophagosome-induction-using-a-bioinformatic-approach
#6
Zarrin Basharat, Sarah Rizwan Qazi, Azra Yasmin, Syed Aoun Ali, Deeba Noreen Baig
Autophagy is crucial for maintaining physiological homeostasis, but its role in infectious diseases is not yet adequately understood. The binding of Anaplasma translocated substrate-1 (ATS1) to the human Beclin1 (BECN1) protein is responsible for the modulation of autophagy pathway. ATS1-BECN1 is a novel type of interaction that facilitates Anaplasma phagocytophilum proliferation, leading to intracellular infection via autophagosome induction and segregation from the lysosome. Currently, there is no report of post translational modifications (PTMs) of BECN1 or cross-talk required for ATS-BECN1 complex formation...
September 13, 2016: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/26601103/systematic-analysis-and-prediction-of-in-situ-cross-talk-of-o-glcnacylation-and-phosphorylation
#7
Heming Yao, Ao Li, Minghui Wang
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue...
2015: BioMed Research International
https://www.readbyqxmd.com/read/25605461/systematic-characterization-and-prediction-of-post-translational-modification-cross-talk
#8
Yuanhua Huang, Bosen Xu, Xueya Zhou, Ying Li, Ming Lu, Rui Jiang, Tingting Li
Post-translational modification (PTM)(1) plays an important role in regulating the functions of proteins. PTMs of multiple residues on one protein may work together to determine a functional outcome, which is known as PTM cross-talk. Identification of PTM cross-talks is an emerging theme in proteomics and has elicited great interest, but their properties remain to be systematically characterized. To this end, we collected 193 PTM cross-talk pairs in 77 human proteins from the literature and then tested location preference and co-evolution at the residue and modification levels...
March 2015: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/25228883/metabolism-leaves-its-mark-on-the-powerhouse-recent-progress-in-post-translational-modifications-of-lysine-in-mitochondria
#9
REVIEW
Kyriakos N Papanicolaou, Brian O'Rourke, D Brian Foster
Lysine modifications have been studied extensively in the nucleus, where they play pivotal roles in gene regulation and constitute one of the pillars of epigenetics. In the cytoplasm, they are critical to proteostasis. However, in the last decade we have also witnessed the emergence of mitochondria as a prime locus for post-translational modification (PTM) of lysine thanks, in large measure, to evolving proteomic techniques. Here, we review recent work on evolving set of PTM that arise from the direct reaction of lysine residues with energized metabolic thioester-coenzyme A intermediates, including acetylation, succinylation, malonylation, and glutarylation...
2014: Frontiers in Physiology
https://www.readbyqxmd.com/read/25175897/sub-proteome-s-nitrosylation-analysis-in-brassica-juncea-hints-at-the-regulation-of-brassicaceae-specific-as-well-as-other-vital-metabolic-pathway-s-by-nitric-oxide-and-suggests-post-translational-modifications-cross-talk
#10
REVIEW
Ankita Sehrawat, Renu Deswal
Abiotic stress affects the normal physiology of the plants and results in crop loss. Brassica juncea is an oil yielding crop affected by abiotic stress. In future, over 30% yield loss by abiotic stress is predicted in India. Understanding the mechanism of plant response to stress would help in developing stress tolerant crops. Nitric oxide (NO) is now viewed as a remarkably important signaling molecule, involved in regulating stress responses. S-Nitrosylation is a NO based post-translational modification (PTM), linked with the regulation of many physiologically relevant targets...
December 1, 2014: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/24997861/accelerated-chromatin-biochemistry-using-dna-barcoded-nucleosome-libraries
#11
Uyen T T Nguyen, Lenka Bittova, Manuel M Müller, Beat Fierz, Yael David, Brian Houck-Loomis, Vanessa Feng, Geoffrey P Dann, Tom W Muir
Elucidating the molecular details of how chromatin-associated factors deposit, remove and recognize histone post-translational modification (PTM) signatures remains a daunting task in the epigenetics field. We introduce a versatile platform that greatly accelerates biochemical investigations into chromatin recognition and signaling. This technology is based on the streamlined semisynthesis of DNA-barcoded nucleosome libraries with distinct combinations of PTMs. Chromatin immunoprecipitation of these libraries, once they have been treated with purified chromatin effectors or the combined chromatin recognizing and modifying activities of the nuclear proteome, is followed by multiplexed DNA-barcode sequencing...
August 2014: Nature Methods
https://www.readbyqxmd.com/read/24891457/histone-h2b-monoubiquitination-roles-to-play-in-human-malignancy
#12
REVIEW
Alexander J Cole, Roderick Clifton-Bligh, Deborah J Marsh
Ubiquitination has traditionally been viewed in the context of polyubiquitination that is essential for marking proteins for degradation via the proteasome. Recent discoveries have shed light on key cellular roles for monoubiquitination, including as a post-translational modification (PTM) of histones such as histone H2B. Monoubiquitination plays a significant role as one of the largest histone PTMs, alongside smaller, better-studied modifications such as methylation, acetylation and phosphorylation. Monoubiquitination of histone H2B at lysine 120 (H2Bub1) has been shown to have key roles in transcription, the DNA damage response and stem cell differentiation...
February 2015: Endocrine-related Cancer
https://www.readbyqxmd.com/read/24821965/ion-channel-regulation-by-protein-s-acylation
#13
REVIEW
Michael J Shipston
Protein S-acylation, the reversible covalent fatty-acid modification of cysteine residues, has emerged as a dynamic posttranslational modification (PTM) that controls the diversity, life cycle, and physiological function of numerous ligand- and voltage-gated ion channels. S-acylation is enzymatically mediated by a diverse family of acyltransferases (zDHHCs) and is reversed by acylthioesterases. However, for most ion channels, the dynamics and subcellular localization at which S-acylation and deacylation cycles occur are not known...
June 2014: Journal of General Physiology
https://www.readbyqxmd.com/read/24441143/system-level-dynamics-of-post-translational-modifications
#14
REVIEW
Aaron S Gajadhar, Forest M White
Attempts to characterize cellular behaviors with static, univariate measurements cannot fully capture biological complexity and lead to an inadequate interpretation of cellular processes. Significant biological insight can be gleaned by considering the contribution of dynamic protein post-translational modifications (PTMs) utilizing systems-level quantitative analysis. High-resolution mass spectrometry coupled with computational modeling of dynamic signal-response relationships is a powerful tool to reveal PTM-mediated regulatory networks...
August 2014: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/24366814/evolution-and-functional-cross-talk-of-protein-post-translational-modifications
#15
REVIEW
Pedro Beltrao, Peer Bork, Nevan J Krogan, Vera van Noort
Protein post-translational modifications (PTMs) allow the cell to regulate protein activity and play a crucial role in the response to changes in external conditions or internal states. Advances in mass spectrometry now enable proteome wide characterization of PTMs and have revealed a broad functional role for a range of different types of modifications. Here we review advances in the study of the evolution and function of PTMs that were spurred by these technological improvements. We provide an overview of studies focusing on the origin and evolution of regulatory enzymes as well as the evolutionary dynamics of modification sites...
2013: Molecular Systems Biology
https://www.readbyqxmd.com/read/24087892/identification-of-enriched-ptm-crosstalk-motifs-from-large-scale-experimental-data-sets
#16
Mao Peng, Arjen Scholten, Albert J R Heck, Bas van Breukelen
Post-translational modifications (PTMs) play an important role in the regulation of protein function. Mass spectrometry based proteomics experiments nowadays identify tens of thousands of PTMs in a single experiment. A wealth of data has therefore become publically available. Evidently the biological function of each PTM is the key question to be addressed; however, such analyses focus primarily on single PTM events. This ignores the fact that PTMs may act in concert in the regulation of protein function, a process termed PTM crosstalk...
January 3, 2014: Journal of Proteome Research
https://www.readbyqxmd.com/read/23807304/synapsin-1-and-tau-reciprocal-o-glcnacylation-and-phosphorylation-sites-in-mouse-brain-synaptosomes
#17
Min Jueng Kang, Chaeyoung Kim, Hyobin Jeong, Byoung-Kyu Cho, Ae Lan Ryou, Daehee Hwang, Inhee Mook-Jung, Eugene C Yi
O-linked N-acetylglucosamine (O-GlcNAc) represents a key regulatory post-translational modification (PTM) that is reversible and often reciprocal with phosphorylation of serine and threonine at the same or nearby residues. Although recent technical advances in O-GlcNAc site-mapping methods combined with mass spectrometry (MS) techniques have facilitated study of the fundamental roles of O-GlcNAcylation in cellular processes, an efficient technique for examining the dynamic, reciprocal relationships between O-GlcNAcylation and phosphorylation is needed to provide greater insights into the regulatory functions of O-GlcNAcylation...
2013: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/23807195/eavesdropping-on-ptm-cross-talk-through-serial-enrichment
#18
COMMENT
Kristofor Webb, Eric J Bennett
No abstract text is available yet for this article.
July 2013: Nature Methods
https://www.readbyqxmd.com/read/23781231/it-takes-two-to-tango-ubiquitin-and-sumo-in-the-dna-damage-response
#19
Serena Bologna, Stefano Ferrari
The complexity of living cells is primarily determined by the genetic information encoded in DNA and gets fully disclosed upon translation. A major determinant of complexity is the reversible post-translational modification (PTM) of proteins, which generates variants displaying distinct biological properties such as subcellular localization, enzymatic activity and the ability to assemble in complexes. Decades of work on phosphorylation have unambiguously proven this concept. In recent years, the covalent attachment of Ubiquitin or Small Ubiquitin-like Modifiers (SUMO) to amino acid residues of target proteins has been recognized as another crucial PTM, re-directing protein fate and protein-protein interactions...
2013: Frontiers in Genetics
https://www.readbyqxmd.com/read/23642229/readout-of-epigenetic-modifications
#20
REVIEW
Dinshaw J Patel, Zhanxin Wang
This review focuses on a structure-based analysis of histone posttranslational modification (PTM) readout, where the PTMs serve as docking sites for reader modules as part of larger complexes displaying chromatin modifier and remodeling activities, with the capacity to alter chromatin architecture and templated processes. Individual topics addressed include the diversity of reader-binding pocket architectures and common principles underlying readout of methyl-lysine and methyl-arginine marks, their unmodified counterparts, as well as acetyl-lysine and phosphoserine marks...
2013: Annual Review of Biochemistry
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