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https://www.readbyqxmd.com/read/29040908/predicting-lysine-glycation-sites-using-bi-profile-bayes-feature-extraction
#1
Zhe Ju, Juhe Sun, Yanjie Li, Li Wang
Glycation is a nonenzymatic post-translational modification which has been found to be involved in various biological processes and closely associated with many metabolic diseases. The accurate identification of glycation sites is important to understand the underlying molecular mechanisms of glycation. As the traditional experimental methods are often labor-intensive and time-consuming, it is desired to develop computational methods to predict glycation sites. In this study, a novel predictor named BPB_GlySite is proposed to predict lysine glycation sites by using bi-profile bayes feature extraction and support vector machine algorithm...
October 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29040725/protein-s-nitrosylation-regulates-xylem-vessel-cell-differentiation-in-arabidopsis
#2
Harunori Kawabe, Misato Ohtani, Tetsuya Kurata, Tomoaki Sakamoto, Taku Demura
Post-translational modifications of proteins have important roles in the regulation of protein activity. One such modification, S-nitrosylation, involves the covalent binding of nitric oxide (NO)-related species to a cysteine residue. Recent work showed that protein S-nitrosylation has crucial functions in plant development and environmental responses. In the present study, we investigated the importance of protein S-nitrosylation for xylem vessel cell differentiation using a forward-genetics approach. We performed ethyl methanesulfonate mutagenesis of a transgenic Arabidopsis 35S::VND7-VP16-GR line in which the activity of VASCULAR-RELATED NAC-DOMAIN7 (VND7), a key transcription factor involved in xylem vessel cell differentiation, can be induced posttranslationally by glucocorticoid treatment, with the goal of obtaining suppressor mutants that failed to differentiate ectopic xylem vessel cells; we named these mutants suppressor of ectopic vessel cell differentiation induced by VND7 (seiv) mutants...
October 13, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29040603/mitosis-specific-acetylation-tunes-ran-effector-binding-for-chromosome-segregation
#3
Xiaoling Bao, Heng Liu, Xing Liu, Ke Ruan, Yonghui Zhang, Zhiyong Zhang, Qi Hu, Ying Liu, Saima Akram, Jiahai Zhang, Qingguo Gong, Wenwen Wang, Xiao Yuan, Jian Li, Lingli Zhao, Zhen Dou, Ruijun Tian, Xuebiao Yao, Jihui Wu, Yunyu Shi
Stable transmission of genetic information during cell division requires faithful mitotic spindle assembly and chromosome segregation. The Ran GTPase plays a key role in mitotic spindle assembly. However, how the generation of a chemical gradient of Ran-GTP at the spindle is coupled to mitotic post-translational modifications has never been characterized. Here, we solved the complex structure of Ran with the nucleotide release factor Mog1 and delineated a novel mitosis-specific acetylation-regulated Ran-Mog1 interaction during chromosome segregation...
October 6, 2017: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/29039980/advances-in-the-chromosome-centric-human-proteome-project-looking-to-the-future
#4
Young-Ki Paik, Gilbert S Omenn, Lydie Lane, Christopher M Overall
The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on "missing proteins (MPs)", which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs...
October 17, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29036931/mass-spectrometric-studies-of-apolipoprotein-proteoforms-and-their-role-in-lipid-metabolism-and-type-2-diabetes
#5
REVIEW
Dobrin Nedelkov
Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies correlating apolipoproteins proteoforms with the specific clinical measures of lipid metabolism and cardiometabolic risk. Targeted mass spectrometric immunoassays toward apolipoproteins A-I, A-II, and C-III were applied on large cross-sectional and longitudinal clinical cohorts...
October 15, 2017: Proteomes
https://www.readbyqxmd.com/read/29036368/proteomic-identification-of-histone-post-translational-modifications-and-proteins-enriched-at-a-dna-double-strand-break
#6
Pingping Wang, Stephanie Byrum, Faith C Fowler, Sangita Pal, Alan J Tackett, Jessica K Tyler
Here, we use ChAP-MS (chromatin affinity purification with mass spectrometry), for the affinity purification of a sequence-specific single-copy endogenous chromosomal locus containing a DNA double-strand break (DSB). We found multiple new histone post-translational modifications enriched on chromatin bearing a DSB from budding yeast. One of these, methylation of histone H3 on lysine 125, has not previously been reported. Among over 100 novel proteins enriched at a DSB were the phosphatase Sit4, the RNA pol II degradation factor Def1, the mRNA export protein Yra1 and the HECT E3 ligase Tom1...
September 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036198/the-homeodomain-interacting-protein-kinase-hpk-1-preserves-protein-homeostasis-and-longevity-through-master-regulatory-control-of-the-hsf-1-chaperone-network-and-torc1-restricted-autophagy-in-caenorhabditis-elegans
#7
Ritika Das, Justine A Melo, Manjunatha Thondamal, Elizabeth A Morton, Adam B Cornwell, Beresford Crick, Joung Heon Kim, Elliot W Swartz, Todd Lamitina, Peter M Douglas, Andrew V Samuelson
An extensive proteostatic network comprised of molecular chaperones and protein clearance mechanisms functions collectively to preserve the integrity and resiliency of the proteome. The efficacy of this network deteriorates during aging, coinciding with many clinical manifestations, including protein aggregation diseases of the nervous system. A decline in proteostasis can be delayed through the activation of cytoprotective transcriptional responses, which are sensitive to environmental stress and internal metabolic and physiological cues...
October 16, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29035787/identification-of-n-linked-glycosylation-sites-in-the-spike-protein-and-their-functional-impact-on-the-replication-and-infectivity-of-coronavirus-infectious-bronchitis-virus-in-cell-culture
#8
Jie Zheng, Yoshiyuki Yamada, To Sing Fung, Mei Huang, Raymond Chia, Ding Xiang Liu
Spike (S) glycoprotein on the viral envelope is the main determinant of infectivity. The S protein of coronavirus infectious bronchitis virus (IBV) contains 29 putative asparagine(N)-linked glycosylation sites. These post-translational modifications may assist in protein folding and play important roles in the functionality of S protein. In this study, we used bioinformatics tools to predict N-linked glycosylation sites and to analyze their distribution in IBV strains and variants. Among these sites, 8 sites were confirmed in the S protein extracted from partially purified virus particles by proteomics approaches...
October 13, 2017: Virology
https://www.readbyqxmd.com/read/29035223/fmprpmf-a-web-implementation-for-protein-identification-by-robust-peptide-mass-fingerprinting
#9
Youyuan Li, Yingping Zhuang
Peptide mass fingerprinting continues to play an important role in current proteomics studies based on its good performance in sample throughput, specificity for single peptides, and insensitive to unexpected post-translational modifications as compared with . Here, we proposed and evaluated the use of feature-matching pattern-based support vector machines (SVMs) for robust protein identification. This approach is now facilitated with an updated web server (fmpRPMF) incorporated with several newly developed or improved modules and workflows allowing identification of proteins from data...
October 13, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29034140/regulation-of-gene-expression-by-translation-factor-eif5a-hypusine-modified-eif5a-enhances-nonsense-mediated-mrna-decay-in-human-cells
#10
Mainul Hoque, Ji Yeon Park, Yun-Juan Chang, Augusto D Luchessi, Tavane D Cambiaghi, Raghavendra Shamanna, Hartmut M Hanauske-Abel, Bart Holland, Tsafi Pe'ery, Bin Tian, Michael B Mathews
Nonsense-mediated mRNA decay (NMD) couples protein synthesis to mRNA turnover. It eliminates defective transcripts and controls the abundance of certain normal mRNAs. Our study establishes a connection between NMD and the translation factor eIF5A (eukaryotic initiation factor 5A) in human cells. eIF5A modulates the synthesis of groups of proteins (the eIF5A regulon), and undergoes a distinctive two-step post-translational modification (hypusination) catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase...
2017: Translation
https://www.readbyqxmd.com/read/29032483/regulation-of-cardiac-voltage-gated-sodium-channel-by-kinases-roles-of-protein-kinases-a-and-c
#11
Ademuyiwa S Aromolaran, Mohamed Chahine, Mohamed Boutjdir
In the heart, voltage-gated sodium (Nav) channel (Nav1.5) is defined by its pore-forming α-subunit and its auxiliary β-subunits, both of which are important for its critical contribution to the initiation and maintenance of the cardiac action potential (AP) that underlie normal heart rhythm. The physiological relevance of Nav1.5 is further marked by the fact that inherited or congenital mutations in Nav1.5 channel gene SCN5A lead to altered functional expression (including expression, trafficking, and current density), and are generally manifested in the form of distinct cardiac arrhythmic events, epilepsy, neuropathic pain, migraine, and neuromuscular disorders...
October 15, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/29032425/heterologous-expression-of-wheat-tarub1-gene-enhances-disease-resistance-in-arabidopsis-thaliana
#12
Yanlin Yang, Wenqiang Wang, Tian Xu, Na Liu, Honggang Wang, Deshun Feng
Expression of TaRUB1 gene in Arabidopsis thaliana elevates the level of disease-related genes in response to pathogen invasion through the accumulation of callose, necrotic cells, and the outbreak of ROS. Ubiquitin (Ub) and ubiquitin-like proteins are highly conserved in sequence and can covalently bind and modify many intracellular proteins which can be recognized and degraded by 26S proteasome. Post-translational modification of proteins has become a hot research spot today. In the previous study, a cDNA of related-to-ubiquitin protein belonged to ubiquitin-like proteins, whose spatial structure comprised Ub and NEDD8, was obtained from wheat SN6306 by suppression-subtractive hybridization and was named TaRUB1...
October 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/29032071/comparing-intestinal-versus-diffuse-gastric-cancer-using-a-peff-oriented-proteomic-pipeline
#13
Helisa Helena Wippel, Marlon Dias Mariano Santos, Milan Avila Clasen, Louise Ulrich Kurt, Fabio Cesar Sousa Nogueira, Carlos Eduardo Carvalho, Thaís Messias McCormick, Guilherme Pinto Bravo Neto, Lysangela Ronalte Alves, Maria da Gloria da Costa Carvalho, Paulo Costa Carvalho, Juliana de Saldanha da Gama Fischer
Gastric cancer is the fifth most common malignant neoplasia and the third leading cause of cancer death worldwide. Mac-Cormick et al. recently showed the importance of considering the anatomical region of the tumor in proteomic gastric cancer studies; more differences were found between distinct anatomical regions than when comparing healthy versus diseased tissue. Thus, failing to consider the anatomical region could lead to differential proteins that are not disease specific. With this as motivation, we compared the proteomic profiles of intestinal and diffuse adenocarcinoma from the same anatomical region, the corpus...
October 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29031766/disulfide-bond-formation-protects-arabidopsis-thaliana-glutathione-transferase-tau-23-from-oxidative-damage
#14
Maria-Armineh Tossounian, Inge Van Molle, Khadija Wahni, Silke Jacques, Kris Gevaert, Frank Van Breusegem, Didier Vertommen, David Young, Leonardo Astolfi Rosado, Joris Messens
BACKGROUND: Glutathione transferases play an important role as detoxifying enzymes. In A. thaliana, elevated levels of reactive oxygen species (ROS), provoked during biotic and abiotic stress, influence the activity of GSTU23. The aim of this study is to determine the impact of oxidative stress on the function and structure of GSTU23. METHODS: The impact of oxidation on the function of GSTU23 was studied using a glutathione transferase biochemical assay and mass spectrometry...
October 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29030023/on-universal-coding-events-in-protein-biogenesis
#15
REVIEW
Vladimir Kubyshkin, Carlos G Acevedo-Rocha, Nediljko Budisa
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by cellular matching with the acceptor units of their cognitive tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code")...
October 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/29029599/liverwiki-a-wiki-based-database-for-human-liver
#16
Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu
BACKGROUND: Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort...
October 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29029401/lysine-methylation-of-fen1-by-set7-is-essential-for-its-cellular-response-to-replicative-stress
#17
Palaniraja Thandapani, Anthony M Couturier, Zhenbao Yu, Xing Li, Jean-François Couture, Shawn Li, Jean-Yves Masson, Stéphane Richard
The DNA damage response (DDR) is central to the cell survival and it requires post-translational modifications, in part, to sense the damage, amplify the signaling response and recruit and regulate DNA repair enzymes. Lysine methylation of histones such as H4K20 and non-histone proteins including p53 has been shown to be essential for the mounting of the DDR. It is well-known that the lysine methyltransferase SET7 regulates the DDR, as cells lacking this enzyme are hypersensitive to chemotherapeutic drugs. To define addition substrates of SET7 involved in the DDR, we screened a peptide array encompassing potential lysine methylation sites from >100 key DDR proteins and identified peptides from 58 proteins to be lysine methylated defining a methylation consensus sequence of [S>K(-2); S>R(-1); K(0)] consistent with previous findings...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29027989/inhibition-of-neddylation-by-mln4924-improves-neointimal-hyperplasia-and-promotes-apoptosis-of-vascular-smooth-muscle-cells-through-p53-and-p62
#18
Tang-Jun Ai, Jian-Yong Sun, Lin-Juan Du, Chaoji Shi, Chao Li, Xue-Nan Sun, Yan Liu, Lihui Li, Zhixiong Xia, Lijun Jia, Jianmiao Liu, Sheng-Zhong Duan
Targeting apoptosis of vascular smooth muscle cells (VSMCs) represents an attractive approach to diminish the occurrence of restenosis. Neddylation is a highly conserved post-translational modification process and inhibition of neddylation has been shown to regulate apoptosis of other cells. However, the impacts of neddylation inhibition on VSMCs and neointimal hyperplasia have not been studied. In our present study, we have shown that MLN4924, a selective inhibitor of NEDD8-activating enzyme (NAE), markedly inhibited neointimal hyperplasia and accumulation of VSMCs, whereas increased apoptosis in the vascular wall...
October 13, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29027792/multifunctional-cytochrome-c-learning-new-tricks-from-an-old-dog
#19
Damián Alvarez-Paggi, Luciana Hannibal, María A Castro, Santiago Oviedo-Rouco, Veronica Demicheli, Veronica Tórtora, Florencia Tomasina, Rafael Radi, Daniel H Murgida
Cytochrome c (cyt c) is a small soluble heme protein characterized by a relatively flexible structure, particularly in the ferric form, such that it is able to sample a broad conformational space. Depending on the specific conditions, interactions, and cellular localization, different conformations may be stabilized, which differ in structure, redox properties, binding affinities, and enzymatic activity. The primary function is electron shuttling in oxidative phosphorylation, and is exerted by the so-called native cyt c in the intermembrane mitochondrial space of healthy cells...
October 13, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29027453/-ubiquitinated-proteomics-research-of-hep3b
#20
Yingzi Qi, Chen Deng, Na Su, Lingqiang Zhang, Ping Xu
Ubiquitination is one of the most major post-translational modifications playing important role in regulation of intra-cellular proteins' stability, degradation, localization and biological activity. However, these proteins are difficult to be detected due to their low abundance, short half-life. In this study, ubiquitin-binding domains (UBDs) were constructed to purify the ubiquitinated proteins from Hep3B cells. Ubiquitinated proteins and sites were detected by LC-MS/MS. A total of 1 900 potential ubiquitinated proteins were identified...
October 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
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