Relevant bibliographies by topics / Post translational modification (PTM)

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Academic literature on the topic 'Post translational modification (PTM)'

Author: Grafiati
Published: 4 June 2021
Last updated: 5 February 2022

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Journal articles on the topic "Post translational modification (PTM)"

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Urasaki, Yasuyo, and Thuc T. Le. "Differentiation of Essential Oils Using Nanofluidic Protein Post-Translational Modification Profiling." Molecules 24, no. 13 (June 27, 2019): 2383. http://dx.doi.org/10.3390/molecules24132383.

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Current methods for the authentication of essential oils focus on analyzing their chemical composition. This study describes the use of nanofluidic protein post-translational modification (PTM) profiling to differentiate essential oils by analyzing their biochemical effects. Protein PTM profiling was used to measure the effects of four essential oils, copaiba, mandarin, Melissa, and turmeric, on the phosphorylation of MEK1, MEK2, and ERK1/2 in the MAPK signaling pathway; Akt and 4EBP1 in the pI3K/Akt/mTOR signaling pathway; and STAT3 in the JAK/STAT signaling pathway in cultured HepG2 cells. The gain or loss of the phosphorylation of these proteins served as direct read-outs for the positive or negative regulatory effects of essential oils on their respective signaling pathways. Furthermore, protein PTM profiling and GC-MS were employed side-by-side to assess the quality of the essential oils. In general, protein PTM profiling data concurred with GC-MS data on the identification of adulterated mandarin, Melissa, and turmeric essential oils. Most interestingly, protein PTM profiling data identified the differences in biochemical effects between copaiba essential oils, which were indistinguishable with GC-MS data on their chemical composition. Taken together, nanofluidic protein PTM profiling represents a robust method for the assessment of the quality and therapeutic potential of essential oils.
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Wang, Duolin, Yanchun Liang, and Dong Xu. "Capsule network for protein post-translational modification site prediction." Bioinformatics 35, no. 14 (December 6, 2018): 2386–94. http://dx.doi.org/10.1093/bioinformatics/bty977.

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Abstract Motivation Computational methods for protein post-translational modification (PTM) site prediction provide a useful approach for studying protein functions. The prediction accuracy of the existing methods has significant room for improvement. A recent deep-learning architecture, Capsule Network (CapsNet), which can characterize the internal hierarchical representation of input data, presents a great opportunity to solve this problem, especially using small training data. Results We proposed a CapsNet for predicting protein PTM sites, including phosphorylation, N-linked glycosylation, N6-acetyllysine, methyl-arginine, S-palmitoyl-cysteine, pyrrolidone-carboxylic-acid and SUMOylation sites. The CapsNet outperformed the baseline convolutional neural network architecture MusiteDeep and other well-known tools in most cases and provided promising results for practical use, especially in learning from small training data. The capsule length also gives an accurate estimate for the confidence of the PTM prediction. We further demonstrated that the internal capsule features could be trained as a motif detector of phosphorylation sites when no kinase-specific phosphorylation labels were provided. In addition, CapsNet generates robust representations that have strong discriminant power in distinguishing kinase substrates from different kinase families. Our study sheds some light on the recognition mechanism of PTMs and applications of CapsNet on other bioinformatic problems. Availability and implementation The codes are free to download from https://github.com/duolinwang/CapsNet_PTM. Supplementary information Supplementary data are available at Bioinformatics online.
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Hernandez-Valladares, Maria, Rebecca Wangen, Frode S. Berven, and Astrid Guldbrandsen. "Protein Post-Translational Modification Crosstalk in Acute Myeloid Leukemia Calls for Action." Current Medicinal Chemistry 26, no. 28 (October 25, 2019): 5317–37. http://dx.doi.org/10.2174/0929867326666190503164004.

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Background: Post-translational modification (PTM) crosstalk is a young research field. However, there is now evidence of the extraordinary characterization of the different proteoforms and their interactions in a biological environment that PTM crosstalk studies can describe. Besides gene expression and phosphorylation profiling of acute myeloid leukemia (AML) samples, the functional combination of several PTMs that might contribute to a better understanding of the complexity of the AML proteome remains to be discovered. Objective: By reviewing current workflows for the simultaneous enrichment of several PTMs and bioinformatics tools to analyze mass spectrometry (MS)-based data, our major objective is to introduce the PTM crosstalk field to the AML research community. Results: After an introduction to PTMs and PTM crosstalk, this review introduces several protocols for the simultaneous enrichment of PTMs. Two of them allow a simultaneous enrichment of at least three PTMs when using 0.5-2 mg of cell lysate. We have reviewed many of the bioinformatics tools used for PTM crosstalk discovery as its complex data analysis, mainly generated from MS, becomes challenging for most AML researchers. We have presented several non-AML PTM crosstalk studies throughout the review in order to show how important the characterization of PTM crosstalk becomes for the selection of disease biomarkers and therapeutic targets. Conclusion: Herein, we have reviewed the advances and pitfalls of the emerging PTM crosstalk field and its potential contribution to unravel the heterogeneity of AML. The complexity of sample preparation and bioinformatics workflows demands a good interaction between experts of several areas.
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Pascovici, Dana, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, and Mehdi Mirzaei. "Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools." International Journal of Molecular Sciences 20, no. 1 (December 20, 2018): 16. http://dx.doi.org/10.3390/ijms20010016.

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Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra—many of which likely harbour PTMs—through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.
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Dunphy, Katie, Paul Dowling, Despina Bazou, and Peter O’Gorman. "Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers." Cancers 13, no. 8 (April 16, 2021): 1930. http://dx.doi.org/10.3390/cancers13081930.

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Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, altering their structure, function and/or localization. Mass spectrometry (MS)-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with a high level of sensitivity and specificity. The low stoichiometry of modified peptides means fractionation and enrichment techniques are often performed prior to MS to improve detection yields. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes, including cell signaling, apoptosis and transcriptional regulation, that contribute to the malignant phenotype. Furthermore, the mechanism of action of many blood cancer therapies, such as kinase inhibitors, involves inhibiting or modulating protein modifications. Continued optimization of protocols and techniques for PTM analysis in blood cancer will undoubtedly lead to novel insights into mechanisms of malignant transformation, proliferation, and survival, in addition to the identification of novel biomarkers and therapeutic targets. This review discusses techniques used for PTM analysis and their applications in blood cancer research.
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Wang, BingHua, Minghui Wang, and Ao Li. "Prediction of post-translational modification sites using multiple kernel support vector machine." PeerJ 5 (April 27, 2017): e3261. http://dx.doi.org/10.7717/peerj.3261.

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Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.
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Chen, Zhen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana Marquez-Lago, André Leier, Tatsuya Akutsu, et al. "Large-scale comparative assessment of computational predictors for lysine post-translational modification sites." Briefings in Bioinformatics 20, no. 6 (October 4, 2018): 2267–90. http://dx.doi.org/10.1093/bib/bby089.

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Abstract Lysine post-translational modifications (PTMs) play a crucial role in regulating diverse functions and biological processes of proteins. However, because of the large volumes of sequencing data generated from genome-sequencing projects, systematic identification of different types of lysine PTM substrates and PTM sites in the entire proteome remains a major challenge. In recent years, a number of computational methods for lysine PTM identification have been developed. These methods show high diversity in their core algorithms, features extracted and feature selection techniques and evaluation strategies. There is therefore an urgent need to revisit these methods and summarize their methodologies, to improve and further develop computational techniques to identify and characterize lysine PTMs from the large amounts of sequence data. With this goal in mind, we first provide a comprehensive survey on a large collection of 49 state-of-the-art approaches for lysine PTM prediction. We cover a variety of important aspects that are crucial for the development of successful predictors, including operating algorithms, sequence and structural features, feature selection, model performance evaluation and software utility. We further provide our thoughts on potential strategies to improve the model performance. Second, in order to examine the feasibility of using deep learning for lysine PTM prediction, we propose a novel computational framework, termed MUscADEL (Multiple Scalable Accurate Deep Learner for lysine PTMs), using deep, bidirectional, long short-term memory recurrent neural networks for accurate and systematic mapping of eight major types of lysine PTMs in the human and mouse proteomes. Extensive benchmarking tests show that MUscADEL outperforms current methods for lysine PTM characterization, demonstrating the potential and power of deep learning techniques in protein PTM prediction. The web server of MUscADEL, together with all the data sets assembled in this study, is freely available at http://muscadel.erc.monash.edu/. We anticipate this comprehensive review and the application of deep learning will provide practical guide and useful insights into PTM prediction and inspire future bioinformatics studies in the related fields.
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Yang, Tangpo, Zheng Liu, and Xiang David Li. "Developing diazirine-based chemical probes to identify histone modification ‘readers’ and ‘erasers’." Chemical Science 6, no. 2 (2015): 1011–17. http://dx.doi.org/10.1039/c4sc02328e.

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Malik, Arshi, Sarah Afaq, Afaf S. Alwabli, and Khalid Al-ghmady. "Networking of predicted post-translational modification (PTM) sites in human EGFR." Bioinformation 15, no. 7 (July 31, 2019): 448–54. http://dx.doi.org/10.6026/97320630015448.

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Arntzen, Magnus Ø., Christoffer Leif Osland, Christopher Rasch-Olsen Raa, Reidun Kopperud, Stein-Ove Døskeland, Aurélia E. Lewis, and Clive S. D'Santos. "POSTMan (POST-translational modification analysis), a software application for PTM discovery." PROTEOMICS 9, no. 5 (March 2009): 1400–1406. http://dx.doi.org/10.1002/pmic.200800500.

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Dissertations / Theses on the topic "Post translational modification (PTM)"

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Dumont, Quentin. "Applications of Ion Mobility Mass Spectrometry - Screening for SUMOylation and Other Post-Translational Modifications." University of Toledo / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1345130293.

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Matsumiya, Nozomi. "Optimization of disulfide mapping using mass spectrometry." Thesis, Kansas State University, 2009. http://hdl.handle.net/2097/1358.

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Master of Science
Biochemistry
John Tomich
One of the important keys to characterize the biological function of a protein is the study of post-translational modification (PTM). Formation of disulfide bond linkages between cysteine residues within a protein is a common PTM which not only contributes to folding and stabilizing the protein structure, but also to accomplishing its native function. Therefore, the study and discovery of structural-functional relationships of expressed proteins using an isolated proteomics approach has been one of the biggest advances within the field of structural biology in recent years. In this study, rapid disulfide bond mapping of freshly obtained equine serum albumin (ESA) was performed using matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Highly sensitive MALDI-TOF MS is commonly used for the investigation of disulfide bond linkages in the proteomics field. However, it has also been known that the presence of disulfide bond linkages absorbs the energy which is created by the cysteine-cysteine kinetic vibration, resulting in a decrease of the instrumental sensitivity. To overcome this problem, the disulfide bond mapping method was optimized by applying a combination of chemical labeling, proteolytic enzymes, and matrices. With the optimized method, we were also able to achieve high protein sequence coverage. Obtaining higher sequence coverage of a protein provides more information about a protein which helps to identify the protein by peptide mass fingerprint (PMF) technique. These analyses eventually contribute to the estimation of the possible PTM sites.
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Diallo, Issa. "Nouvelle méthode en protéomique pour améliorer l'identification et la quantification des protéines acétylées." Thesis, Université Grenoble Alpes (ComUE), 2017. http://www.theses.fr/2017GREAS035.

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L'acétylation des protéines constitue l’une des plus importantes modifications post-traductionnelles (PTMs). Elle intervient dans de multiples processus bologiques et physiopathologiques tels que, l’activité transcriptionnelle, l'apoptose, la régulation des voies métaboliques, les cancers, les maladies inflammatoires et cardiovasculaires. Face à l’importance de l’acétylation des protéines, il apparaît donc indispensable de bien comprendre les mécanismes qui y sont associés, et donc, de pouvoir identifier et quantifier les protéines acétylées à partir du protéome complet d’échantillons complexes tels que des extraits cellulaires ou tissulaires. La spectrométrie de masse est une technique de choix pour de telles études, car elle permet d’identifier les protéines et les sites d’acétylation, mais aussi de les quantifier en l’associant à des techniques de quantification (label free, SILAC, iTRAQ/TMT, AQUA). Malheureusement, ces méthodes ne ciblent pas particulièrement les acétylations et requièrent l’utilisation de techniques d’enrichissement ou de fractionnement qui ne sont dédiées qu’à certains types d’acetylation : les N-ter et K-acetylation. Aucun enrichissement n’est disponible pour les O- acétylations et ces méthodes d’enrichissement ne sont pas toujours compatibles avec les techniques de quantification citées ci-dessus. Pour améliorer la détection et la quantification des acétylations, nous proposons la méthode RAQIAT (Relatif Absolute Quantification Isobaric Affinity Tag) qui se résume en trois grandes étapes: i) Le blocage des fonctions amines libres à l'aide de la di-méthylation réductrice, ceci empêchera ces dernières de réagir avec le réactif RAQIAT, ii) La désacétylation des lysines acétylées pour permettre une quantification sélective des acétylations, iii) Le marquage des amines primaires précédemment désacétylées dans l’étape 2 par le réactif RAQIAT pour permettre leurs identifications et quantifications. Ce manuscrit a porté en partie sur les deux premières étapes de la méthode RAQIAT.Dans la première étape, les échantillons de protéines de levure ont été digérés puis di-méthylés et fractionnés par OFFGEL en 24 fractions. Ensuite, chacune de ces 24 fractions OFFGEL a été soumise à un fractionnement nano-RPLC et analysée par MALDI TOF/TOF (4800 MALDI-TOF/TOF, Sciex). En parallèle, la même expérience a été réalisée, cette fois-ci sans di-méthylation. L'analyse des données a été réalisée en utilisant le logiciel Mascot comme moteur de recherche.L’efficacité de la réaction de di-méthylation démontrée, nous avons montré que sans réaliser la di-méthylation réductrice 164 sites acétylés ont pu été identifiés alors que 385 sites acétylés distincts ont été identifiés avec la di-méthylation réductrice. De plus, l'amélioration de la détection de l'acétylation en utilisant la méthode de di-méthylation a été observée pour chacune des différents types acétylations: N-ter, K- et O-acétylation.Dans la deuxième étape, nous avons présenté des résultats préliminaires de déacétylation par la sirtuine 1 en présence du peptide de la p53 (Ac-Arg-His-Lys-Lys-(Ac)-AMC) connu comme étant un substrat de cette enzyme. Nous avons observé la formation d’un peptide non acétylé, suggérant une déacétylation de ce peptide acétylé de p53. Cependant, la formation de cet ion étant très faible et l’ion acétylé étant fortement préservé, nous en avons conclu que l’efficacité de la déacétylation du peptide de p53 n’était pas suffisante pour l’intégrer à la méthode RAQIAT
Protein acetylation is one of the most widespread post-translational modifications which is involved in many cellular physiologies and pathologies such as cancers. Regarding the important biological effect of protein acetylation and a non-negligible number of proteins bearing this PTM, several methods emerged last decade to investigate such PTM. But the detection of acetylations and their quantification are still limited and enrichment method allowing a better detection of acetylation target mostly one kind of acetylation (K-acetylation). To improve the detection of the three kind of acetylation (N-ter, K, and O-) and their quantification, we propose the RAQIAT method (Relative Absolute Quantification Isobaric Affinity Tag), based on protein digestion followed by 3 steps : i) a protection of free primary amines at N-ter, lysine (i.e. primary amine not bearing PTM) based on a reductive di-methylation strategy ii) a deacetylation of acetylated residues to obtain free primary amine corresponding to peptides previously acetylated iii) a RAQIAT labeling on the free primary amine obtained in the previous step to allow the enrichment of peptides previously acetylated and their quantifications. Herein, we present the investigation of the two first steps of RAQIAT method.In the first step, we evidenced that the reductive di-methylation strategy improved the detection of the three kind of acetylation: N-ter, K- and O- acetylations. Yeast protein samples were digested with trypsin prior di-methylation of resulting peptide mixture. Then, di-methylated peptide mixtures were fractionated by OFFGEL and reverse phase liquid chromatography followed by MALDI-TOF/TOF mass spectrometry analysis. Data analysis was performed by using Mascot as search engines.Our results showed that OFFGEL fractionation is a useful step to increase detection of acetylations. Moreover, we showed that our di-methylation treatment improved significantly detection of acetylation. Indeed, after di-methylation treatment, 385 unique acetylated sites were identified while 164 unique acetylated peptides were detected without di-methylation treatment. The improvement of acetylation detection using our di-methylation strategy is observed for each of acetylations: N-ter, K- and O-acetylations. Thus, this new proteomic method is promising to enhance N-ter, K- and O-acetylation detection.In the second step, we presented preliminary results of deacetylation by sirtuin 1 in the presence of p53 peptide (Ac-Arg-His-Lys-Lys- (Ac) –AMC. However, the low deacetylation efficiency of the p53 peptide observed, conclude that is not suitable to applicate into RAQIAT Method
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Schiller, Rachel Shamo. "Investigating the inhibitor and substrate diversity of the JmjC histone demethylases." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:1e7fd2a1-a9c3-48f7-8fa7-a041299d42f9.

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Epigenetic control of gene expression by histone post-translational modifications (PTMs) is a complex process regulated by proteins that can 'read', 'write' or 'erase' these PTMs. The histone lysine demethylase (KDM) family of epigenetic enzymes remove methyl modifications from lysines on histone tails. The Jumonji C domain (JmjC) family is the largest family of KDMs. Investigating the scope and mechanisms of the JmjC KDMs is of interest for understanding the diverse functions of the JmjC KDMs in vivo, as well as for the application of the basic science to medicinal chemistry design. The work described in this thesis aimed to biochemically investigate the inhibitor and substrate diversity of the JmjC KDMs, it led to the identification of new inhibitors and substrates and revealed a potential combinatorial dependence between adjacent histone PTMs. Structure-activity relationship studies gave rise to an n-octyl ester form of IOX1 with improved cellular potency and selectivity towards the KDM4 subfamily. This compound should find utility as a basis for the development of JmjC inhibitors and as a tool compound for biological studies. The rest of this thesis focused on the biochemical investigations of potential substrates and inhibitors for KDM3A, a JmjC demethylase with varied physiological functions. Kinetic characterisation of reported KDM3A substrates was used as the basis for evaluations of novel substrates and inhibitors. Further studies found TCA cycle intermediates to be moderate co-substrate competitive inhibitors of KDM3A. Biochemical investigations were carried out to study potential protein-protein interactions of KDM3A with intraflagellar transport proteins (IFTs), non-histone proteins involved in the formation of sperm flagellum. Work then addressed the exploration of novel in vitro substrates for KDM3 (KDM3A and JMJD1C) mediated catalysis, including: methylated arginines, lysine analogues, acetylated and formylated lysines. KDM3A, and other JmjC KDMs, were found to catalyse novel arginine demethylation reaction in vitro. Knowledge gained from studies with unnatural lysine analogues was utilised to search for additional novel PTM substrates for KDM3A. These results constitute the first evidence of JmjC KDM catalysed hydroxylation of an Nε-acetyllysine residue. The H3 K4me3 position seems to be required for acetyllysine substrate recognition, implying a combinatorial effect between PTMs. Preliminary results provide evidence that JMJD1C, a KDM3 protein previously reported to be inactive, may catalyse deacetylation in vitro. An additional novel reaction, observed with both KDM3A and JMJD1C, is deformylation of Nε-formyllysine residues on histone H3 fragment peptides. Interestingly, H3 K4 methylation was also observed to enhance the apparent deformylation of both KDM3A and JMJD1C catalysed reactions. Overall, findings in this thesis suggest that the catalytic activity of JmjC KDMs extends beyond lysine demethylation. In a cellular context, members of the KDM3 subfamily might provide a regulatory link between methylation and acylation marks. Such a link will further highlight the complex relationships between histone PTMs and the epigenetic enzymes that regulate them. The observed dependency of H3 K9 catalysis on H3 K4 methylation adds another layer of complexity to the epigenetic regulation by histone PTMs.
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Gopalswamy, Mohanraj [Verfasser]. "Aggregation and post-translational modification of the parathyroid hormone and its agonistic activity towards the G-protein coupled PTH receptors / Mohanraj Gopalswamy." Halle, 2017. http://d-nb.info/1141177951/34.

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Dedieu, Alain. "Exploration des modifications post-traductionnelles des protéines : nouvelles approches et nouveaux modèles biologiques." Thesis, Montpellier 1, 2014. http://www.theses.fr/2014MON13516/document.

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L'étude des modifications post-traductionnelles a connu au cours des dernières années un regain d'intérêt notable. Tout d'abord car elle s'effectue aujourd'hui au travers d'approches basées sur la spectrométrie de masse, technique qui pendant cette période a connu de profonds bouleversements, conduisant à des études plus aisées et systématiques.Mais aussi car tant par leur variété que par le rôle qu'elles jouent dans la vie et la régulation cellulaire, ces modifications ne peuvent plus être négligées. Par ailleurs au cours de ces quinze dernières années, nous avons assisté concernant les procaryotes à un changement total de paradigme. En effet à la fin des années 90, l'idée dominante était que ces modifications pouvaient exister chez ceux-ci mais de façon très partielle et/ou très particulière.Dans ce travail, les divers degrés d'iodation de la tyrosine ont été sondés par une approche de type «shotgun » sur un organe entier, la thyroïde de souris. L'efficacité de ce type d'approche démontrée, les modifications post-traductionnelles potentiellement présentes dans des organismes modèles radiorésistants, la bactérie Deinococcus deserti et l'archée Thermococcus gammatolerans ont été analysées. Dans le premier cas, les données de protéomique montrent que de nombreuses acétylations N-terminales portent sur un motif spécifique (essentiellement des thréonines et sérines), cas très atypique pour une bactérie. Chez Thermococcus gammatolerans les acétylations N-terminales sont rares, mais la présence d'acétylations sur les chaînes latérales des lysines est notable. La présence de phosphorylations sur ces mêmes protéines, laisse entrevoir un possible phénomène de « cross talk » entre les lysines acétylées et les sérines et/ou thréonines phosphorylées.Ici, nous démontrons que la complexité du protéome chez les procaryotes par le biais des MPT est bien réelle et que de possibles interdépendances entre MPT mériteraient un regard nouveau
Recently, the study of post-translational modifications has greatly evolved, mainly because of crucial progresses in mass spectrometry methodology which have allowed high-throughput, high resolution analysis. Their variety and their role in the regulation of key molecular mechanisms are increasingly documented. In this work, the different degrees of iodination of tyrosine were probed with a "shotgun" approach carried out from an entire organ, the mice thyroid. Post-translational modifications present in two radioresistant organism models, the bacterium Deinococcus deserti and the archaeon Thermococcus gammatolerans, were analyzed. The large scale exploration of N-terminal acetylation in D. deserti indicates a specific pattern of this modification on serine and threonine, as well as an atypical, high propension to acetylation with 50% of modified N-termini. In T. gammatolerans, N-terminal acetylation is rare, but the presence of acetylation on lysine side chains is significant. The presence of phosphorylation on these proteins suggests a potential "cross talk" between the acetylated lysine and phosphorylated serine or threonine residues. This work demonstrates that the complexity of the proteome in prokaryotes through post-translational modifications is higher than expected when extremophiles are scrutinized compared to classical prokaryote models. Interdependencies between post-translational modifications definitively deserve a fresher look
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Gibson, Matthew D. "Reading the Epigenetic State of Chromatin Alters its Accessibility." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480534756664384.

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Silverman, H. S. "Post-translational modification of mucins." Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365785.

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Inche, Adam. "The post translational modification of the retinoblastoma protein." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.491620.

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The retinoblastoma protein (pRb) is a central figure in the control of not only the cell cycle, but also other cellular functions such as differentiation. The regulation of pRb function is through a variety of post translational modifications, either on pRb itself, or by the controlling influence of pRb on the post translational modification of the histone proteins. Phosphorylation of pRb is a key mechanism in the regulation of the cell cycle. pRb is also involved in the recruitment of histone methyltransferase (HMT) and acetyltransferase (HAT) to the chromatin to modify histones. Previous work within the group showed that pRb was subjected to acetylation by the HAT p300. The acetylation of pRb was shown to negatively influence phosphorylation by interfering with a proposed kinase binding site. Another group showed that acetylation of pRb may also be involved in the differentiation of myoblast cells. The work presented here characterises, for the first time, the methylation of pRb by the HMT Set7/9, previously shown to methylate p53. This post translational modification was identified by a combination of ill vitro mutational analysis and mass spectroscopy. The site of methylation was shown to be at lysine 873 (K873), the same region that was subjected to acetylation by the HAT p300. It was also shown that methylation at K873 occurs il1 vivo and is up regulated in response to myoblast differentiation. The ability for these cells to differentiate is compromised when a mutant of pRb is used that cannot be methylated at position 873. . The methylation ofpRb also seems to exert a regulatory control over other post translational modifications that occur on pRb. It was shown that pRb methylated by Set7/9 was able to reduce -acetylation at positions 873/4. The over expression of Set7/9 in cells was also shown to specifically negatively affect the phosphorylation of S811. This site has been implicated in the regulation cell cycle exit, and therefore supports the theory that methylation of pRb is required for the progression of differentiation. It is unclear at this time if the regulation of phosphorylation at S811 is as a consequence of methylation at K873, or at a secondary site that was identified by in vitro mass spectroscopy at K810.
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Strong, Emily. "Post translational modification of Exo1 in Saccharomyces cerevisiae." Thesis, University of Sheffield, 2017. http://etheses.whiterose.ac.uk/19163/.

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Meiosis is the cell division that produces haploid gametes for the purpose of sexual reproduction. During this division it is essential for homologous chromosomes to be securely paired and segregated in order for the gametes to receive a single copy of each chromosome. An important protein in this process is the exonuclease Exo1. Exo1 has two important and distinct roles during meiosis: resection of DNA at double-strand breaks (DSBs) exposing single stranded DNA suitable for strand invasion, and resolution of double-Holliday junctions (dHJs) as cross-overs. Exo1 also acts as a nuclease during DSB repair during mitosis. Previous studies have shown that Exo1 is phosphorylated in response to DNA damage in mitotically cycling cells. The role of this phosphorylation is yet to be definitively determined. This study aimed to test the hypothesis that Exo1 might also be phosphorylated in response to meiotic DSBs. It was confirmed that Exo1 was phosphorylated in response to mitotic DNA damage by designing a tagged version of Exo1 in the Saccharomyces cerevisiae background SK1, a strain commonly used for meiotic experiments. Meiotic progression and spore viability appeared to be normal in cells with exo1 mutated at the phosphorylation sites reported as active in mitosis. In meiotic studies Exo1 was found to be phosphorylated during meiosis, and this phosphorylation was different to that seen in previous mitotic studies. It was found that this phosphorylation was transient during meiosis and that it reflected the presence of Spo11-DSBs and their repair.
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Books on the topic "Post translational modification (PTM)"

1

Kannicht, Christoph, ed. Post-Translational Modification of Proteins. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9055-9.

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Walsh, Gary. Post-translational modification of protein biopharmaceuticals. Weinheim: Wiley-VCH, 2009.

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Brodbeck, Urs, and Clement Bordier, eds. Post-translational Modification of Proteins by Lipids. Berlin, Heidelberg: Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-74009-1.

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Posttranslational modification of proteins: Expanding nature's inventory. Englewood, Colo: Roberts and Co. Publishers, 2006.

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Post-translational modifications in health and disease. New York: Springer, 2010.

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1959-, Martin Bruce L., and Wang Jerry H, eds. Co- and post-translational modification of proteins: Chemical principles and biological effects. New York: Oxford University Press, 1994.

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Troit͡skiĭ, G. V. Defektnye belki: Postsinteticheskai͡a modifikat͡sii͡a. Kiev: Nauk. dumka, 1991.

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International, EBSA Symposium (2nd 1988 Gwatt Switzerland). Cytoskeletal and extracellular proteins: Structure, interaction, and assembly. Berlin: Springer-Verlag, 1989.

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NATO Advanced Study Institute on Cellular Regulation by Protein Phosphorylation (1990 La Londe les Maures, France). Cellular regulation by protein phosphorylation. Berlin: Springer-Verlag, 1991.

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SUMO regulation of cellular processes. Dordrecht: Springer, 2009.

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Book chapters on the topic "Post translational modification (PTM)"

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Holtz, Anja, Nathan Basisty, and Birgit Schilling. "Quantification and Identification of Post-Translational Modifications Using Modern Proteomics." In Methods in Molecular Biology, 225–35. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1024-4_16.

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AbstractPost-translational modifications (PTMs) occur dynamically, allowing cells to quickly respond to changes in the environment. Lysine residues can be targeted by several modifications including acylations (acetylation, succinylation, malonylation, glutarylation, and others), methylation, ubiquitination, and other modifications. One of the most efficient methods for the identification of post-translational modifications is utilizing immunoaffinity enrichment followed by high-resolution mass spectrometry. This workflow can be coupled with comprehensive data-independent acquisition (DIA) mass spectrometry to be a high-throughput, label-free PTM quantification approach. Below we describe a detailed protocol to process tissue by homogenization and proteolytically digest proteins, followed by immunoaffinity enrichment of lysine-acetylated peptides to identify and quantify relative changes of acetylation comparing different conditions.
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Nicosia, Luciano, and Tiziana Bonaldi. "Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions." In Methods in Molecular Biology, 251–74. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1597-3_14.

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McAllister-Williams, R. Hamish, Daniel Bertrand, Hans Rollema, Raymond S. Hurst, Linda P. Spear, Tim C. Kirkham, Thomas Steckler, et al. "Post-Translational Modification." In Encyclopedia of Psychopharmacology, 1052–53. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_1545.

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Wang, Jun, and Robert J. Schwartz. "Post-translational Modification." In Congenital Heart Diseases: The Broken Heart, 173–202. Vienna: Springer Vienna, 2016. http://dx.doi.org/10.1007/978-3-7091-1883-2_14.

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McAllister-Williams, R. Hamish, Daniel Bertrand, Hans Rollema, Raymond S. Hurst, Linda P. Spear, Tim C. Kirkham, Thomas Steckler, et al. "Post-Translational Protein Modification." In Encyclopedia of Psychopharmacology, 1053. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_4474.

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McAllister-Williams, R. Hamish, Daniel Bertrand, Hans Rollema, Raymond S. Hurst, Linda P. Spear, Tim C. Kirkham, Thomas Steckler, et al. "Post-Translational Amino Acid Modification." In Encyclopedia of Psychopharmacology, 1052. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_4473.

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Krishna, Radha G., and Finn Wold. "Post-Translational Modification of Proteins." In Advances in Enzymology - and Related Areas of Molecular Biology, 265–98. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/9780470123133.ch3.

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Ivanisenko, Vladimir A., Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Dmitry A. Afonnikov, and Nikolay A. Kolchanov. "Web-Based Computational Tools for the Prediction and Analysis of Posttranslational Modifications of Proteins." In Post-Translational Modification of Proteins, 1–20. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9055-9_1.

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Azzouz, Nahid, Peter Gerold, and Ralph T. Schwarz. "Metabolic Labeling and Structural Analysis of Glycosylphosphatidylinositols from Parasitic Protozoa." In Post-Translational Modification of Proteins, 145–62. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9055-9_10.

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Lenz, Christof. "Identification of Protein Phosphorylation Sites by Advanced LC-ESI-MS/MS Methods." In Post-Translational Modification of Proteins, 163–78. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9055-9_11.

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Conference papers on the topic "Post translational modification (PTM)"

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Cao, Zhendong, Krista A. Budinich, Hua Huang, Bin Lu, Zhen Zhang, Diqiu Ren, Yeqiao Zhou, et al. "Abstract LB205: The IRF8-MEF2D transcription factor circuit regulated by a druggable multiple post-translational modification (PTM) reader ZMYND8 in acute myeloid leukemia." In Proceedings: AACR Annual Meeting 2021; April 10-15, 2021 and May 17-21, 2021; Philadelphia, PA. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1538-7445.am2021-lb205.

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Kannan, Surya, and Serhiy Souchelnytski. "Post-Translational Modifications of Albumin in Cancer – A Rich Source for Diagnostic and Monitoring of Treatment." In Qatar University Annual Research Forum & Exhibition. Qatar University Press, 2020. http://dx.doi.org/10.29117/quarfe.2020.0171.

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Albumin is in contact with all cells in a body. This major protein in a plasma accesses all tissues and organs and has a number of different roles. Albumin was found to have more than 50 posttranslational modifications (PTMs). Some of the albumin PTMs showed correlation with tumorigenesis. Examples of PTMs of albumin are reported at www.phosphosite.org. Modifications like glycation of patients with breast cancer is seen higher as compared to healthy control. We hypothesize that several novel post-translational modification in albumin could be related to cancer and can be used as biomarkers. We performed mass spectrometry and 2D gel electrophoresis analysis of serum albumin for 32 most common PTMs. We identified most of these PTMs in albumin. We observed that human cancer cells affected PTMs profile of albumin. Examples of affected PTMs are phosphorylation, palmitolylation, geranyl- geranylation etc. We observed also differences in PTMs profiles of albumin from serum of a healthy person and cancer patient. O - GlcNAcylation, farnesylation, glutathionylation, S- nitrosylation etc PTMs were found to differ. Our data show that PTMs of albumin can be easily detected. Our trial with 32 PTMs can be expanded to detect up to a hundred known PTMs. These PTMs may correlate with cancer development, and may be used as markers in cancer diagnostic and prognostic.
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Toes, R. "SP0155 The role of post-translational modification and autoreactivity." In Annual European Congress of Rheumatology, 14–17 June, 2017. BMJ Publishing Group Ltd and European League Against Rheumatism, 2017. http://dx.doi.org/10.1136/annrheumdis-2017-eular.7219.

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Meng, Peng, and Rita Ghosh. "Abstract 4208: Post-translational modification of E2F1 in malignant melanoma." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-4208.

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Wang, Duolin, and Dongpeng Liu. "MusiteDeep: A deep-learning framework for protein post-translational modification site prediction." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8218046.

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Cleland, Timothy Paul, Elena R. Schroeter, Robert S. Feranec, and Deepak Vashishth. "PROTEIN AND POST-TRANSLATIONAL MODIFICATION PRESERVATION IN CASTOROIDES OHIOENSIS FROM NEW YORK." In GSA Annual Meeting in Denver, Colorado, USA - 2016. Geological Society of America, 2016. http://dx.doi.org/10.1130/abs/2016am-285233.

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Baker, Rachael, Aaron Hobbs, Minh Huynh, Atsuo Sasaki, Henrik Dohlman, and Sharon L. Campbell. "Abstract IA18: Activation of RAS by post-translational modification: Ubiquitination and thiol oxidation." In Abstracts: AACR Special Conference on RAS Oncogenes: From Biology to Therapy; February 24-27, 2014; Lake Buena Vista, FL. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1557-3125.rasonc14-ia18.

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Ito, Tatsuo, Zhao Xinyang, Yoshiyuki Suehara, Akira Kawai, Stephen D. Nimer, and Marc Ladanyi. "Abstract LB-172: Role of post-translational modification of the RUNX2 transcription factor in osteosarcoma." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-lb-172.

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Casey, J. L., L. Gu, D. Davis, G. Q. Cai, Q. Ding, and A. B. B. Carter. "Oxidant-Mediated Transcription and Post-Translational Modification of PGC-1α Is Required for Fibrotic Repair." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a7874.

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Santhosh, K. T., Sai Prasad Pydi, Prashen Chelikani, and Shyamala Dakshinamurti. "Serine Phosphorylation: An Important Post-translational Modification For Functional Regulation Of Smooth Muscle Thromboxane Receptor." In American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans. American Thoracic Society, 2010. http://dx.doi.org/10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a6361.

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Reports on the topic "Post translational modification (PTM)"

1

Podlevsky, Joshua. Cas9 Protein Post-translational Modifications (PTMs): A Potential Biomarker of Gene-editing. Office of Scientific and Technical Information (OSTI), October 2019. http://dx.doi.org/10.2172/1571552.

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DeCastro, Andrew J., Pratima Cherukuri, and James DiRenzo. Regulation of Mammary Stem Cell Quiescence via Post-Translational Modification of DeltaNp63alpha. Fort Belvoir, VA: Defense Technical Information Center, December 2012. http://dx.doi.org/10.21236/ada576304.

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DeCastro, Andrew J., Pratima Cherukuri, and James DiRenzo. Regulation of Mammary Stem Cell Quiescence via Post-Translational Modification of DeltaNp63alpha. Fort Belvoir, VA: Defense Technical Information Center, February 2014. http://dx.doi.org/10.21236/ada599224.

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Eichler, Jerry. Protein Glycosylation in Archaea: A Post-Translational Modification to Enhance Extremophilic Protein Stability. Fort Belvoir, VA: Defense Technical Information Center, January 2010. http://dx.doi.org/10.21236/ada515568.

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Chen, J. D. Obstructing Androgen Receptor Activation in Prostate Cancer Cells Through Post-translational Modification by NEDD8. Fort Belvoir, VA: Defense Technical Information Center, November 2012. http://dx.doi.org/10.21236/ada582181.

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Chen, J. D. Obstructing Androgen Receptor Activation in Prostate Cancer Cells Through Post-translational Modification by NEDD8. Fort Belvoir, VA: Defense Technical Information Center, May 2011. http://dx.doi.org/10.21236/ada553448.

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