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Post translational modifications

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https://www.readbyqxmd.com/read/29150361/post-translational-mechanisms-of-host-subversion-by-bacterial-effectors
#1
REVIEW
Nichollas E Scott, Elizabeth L Hartland
Bacterial effector proteins are a specialized class of secreted proteins that are translocated directly into the host cytoplasm by bacterial pathogens. Effector proteins have diverse activities and targets, and many mediate post-translational modifications of host proteins. Effector proteins offer potential in novel biotechnological and medical applications as enzymes that may modify human proteins. Here, we discuss the mechanisms used by effectors to subvert the human host through blocking, blunting, or subverting immune mechanisms...
November 14, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/29149817/high-density-lipoprotein-hdl-dysfunction-and-future-of-hdl
#2
Sibel Ertek
Although high density lipoprotein cholesterol (HDL-C) levels are inversely proportional to cardiovascular risk in many studies, recent pharmacological interventional studies with HDL-C raising strategies did not show a benefit in terms of vascular events. The HDL particle is heterogenous with anti-atherogenic functions and non-vascular effects. Many factors affect HDL components and may either cause compositional changes, post-translational modifications of proteins, or alter lipids and other cargo molecules; generally these factors cause more than one of these changes, resulting in functional differences...
November 16, 2017: Current Vascular Pharmacology
https://www.readbyqxmd.com/read/29149100/bcl-2-family-proteins-changing-partners-in-the-dance-towards-death
#3
REVIEW
Justin Kale, Elizabeth J Osterlund, David W Andrews
The BCL-2 family of proteins controls cell death primarily by direct binding interactions that regulate mitochondrial outer membrane permeabilization (MOMP) leading to the irreversible release of intermembrane space proteins, subsequent caspase activation and apoptosis. The affinities and relative abundance of the BCL-2 family proteins dictate the predominate interactions between anti-apoptotic and pro-apoptotic BCL-2 family proteins that regulate MOMP. We highlight the core mechanisms of BCL-2 family regulation of MOMP with an emphasis on how the interactions between the BCL-2 family proteins govern cell fate...
November 17, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29148315/sumoylation-in-brain-ischemia-patterns-targets-and-translational-implications
#4
Joshua D Bernstock, Wei Yang, Daniel G Ye, Yuntian Shen, Stefano Pluchino, Yang-Ja Lee, John M Hallenbeck, Wulf Paschen
Post-translational protein modification by small ubiquitin-like modifier (SUMO) regulates a myriad of homeostatic and stress responses. The SUMOylation pathway has been extensively studied in brain ischemia. Convincing evidence is now at hand to support the notion that a major increase in levels of SUMOylated proteins is capable of inducing tolerance to ischemic stress. Therefore, the SUMOylation pathway has emerged as a promising therapeutic target for neuroprotection in the face of brain ischemia. Despite this, it is prudent to acknowledge that there are many key questions still to be addressed in brain ischemia related to SUMOylation...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/29147901/expression-of-dj-1-in-neurodegenerative-disorders
#5
Daria Antipova, Rina Bandopadhyay
In 2003, autosomal recessive loss-of-function mutations were identified in PARK7 gene that caused early-onset Parkinson's disease (PD). The PARK7 gene encodes a conserved protein termed DJ-1. DJ-1 is a ubiquitous protein, and within the brain, it is present in the nucleus and cytoplasm of both neuronal and glial cells. DJ-1 is a multifunctional protein, and numerous studies have ascribed various roles, including antioxidative properties, chaperone function, protease activities, mitochondrial functions and regulation of transcription to the protein...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29146736/quantitative-high-throughput-screening-identifies-cytoprotective-molecules-that-enhance-sumo-conjugation-via-the-inhibition-of-sumo-specific-protease-senp-2
#6
Joshua D Bernstock, Daniel Ye, Jayden A Smith, Yang-Ja Lee, Florian A Gessler, Adam Yasgar, Jennifer Kouznetsova, Ajit Jadhav, Zhuoran Wang, Stefano Pluchino, Wei Zheng, Anton Simeonov, John M Hallenbeck, Wei Yang
The development of novel neuroprotective treatments for acute stroke has been fraught with failures, which supports the view of ischemic brain damage as a highly complex multifactorial process. Post-translational modifications such as small ubiquitin-like modifier (SUMO)ylation have emerged as critical molecular regulatory mechanisms in states of both homeostasis and ischemic stress, as evidenced by our previous work. Accordingly, the clinical significance of the selective control of the global SUMOylation process has become apparent in studies of ischemic pathobiology and pathophysiology...
November 16, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29145615/iptmnet-an-integrated-resource-for-protein-post-translational-modification-network-discovery
#7
Hongzhan Huang, Cecilia N Arighi, Karen E Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K Vijay-Shanker, Cathy H Wu
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, employing an integrative bioinformatics approach-combining text mining, data mining, and ontological representation to capture rich PTM information, including PTM enzyme-substrate-site relationships, PTM-specific protein-protein interactions (PPIs) and PTM conservation across species...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145159/potential-link-between-m-6-a-modification-and-systemic-lupus-erythematosus
#8
REVIEW
Lian-Ju Li, Yin-Guang Fan, Rui-Xue Leng, Hai-Feng Pan, Dong-Qing Ye
The field of m(6)A modification and epitranscriptomics has recently attracted much attention. More methods allowing for precise m(6)A site profiling and location are developed and crucial players of m(6)A modification machinery are increasingly identified. Although some challenges remain, m(6)A modification is found to modulate almost all aspects of RNA metabolism, such as splicing, stability, structure, translation, and export. Thus, m(6)A modification adds a new layer of post-transcriptional gene expression regulation, and it is implicated in T cell response to HIV infection, type I interferon production, and T cell differentiation and homeostasis...
November 13, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29144135/parameterization-of-palmitoylated-cysteine-farnesylated-cysteine-geranylgeranylated-cysteine-and-myristoylated-glycine-for-the-martini-force-field
#9
Yoav Atsmon-Raz, D Peter Tieleman
Peripheral membrane proteins go through various post-translational modifications that covalently bind fatty acid tails to specific amino acids. These post translational modifications significantly alter the lipophilicity of the modified proteins and allow them to anchor to biological membranes. Over 1000 different proteins have been identified to date that require such membrane-protein interactions in order to carry out their biological functions, including members of the Src and Ras superfamilies that play key roles in cell signaling and carcinogenesis...
November 16, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29143554/the-octanoylated-energy-regulating-hormone-ghrelin-an-expanded-view-of-ghrelin-s-biological-interactions-and-avenues-for-controlling-ghrelin-signaling
#10
Elizabeth R Cleverdon, Kayleigh R McGovern-Gooch, James L Hougland
Ghrelin is a small peptide hormone that requires a unique post-translational modification, serine octanoylation, to bind and activate the GHS-R1a receptor. Initially demonstrated to stimulate hunger and appetite, ghrelin-dependent signaling is implicated in a variety of neurological and physiological processes influencing diseases such as diabetes, obesity, and Prader-Willi syndrome. In addition to its cognate receptor, recent studies have revealed ghrelin interacts with a range of binding partners within the bloodstream...
November 16, 2017: Molecular Membrane Biology
https://www.readbyqxmd.com/read/29142256/quantitative-analysis-of-protein-protein-interactions-and-post-translational-modifications-in-rare-immune-populations
#11
Ayelet Avin, Maayan Levy, Ziv Porat, Jakub Abramson
In spite of recent advances in proteomics, quantitative analyses of protein-protein interactions (PPIs) or post-translational modifications (PTMs) in rare cell populations remain challenging. This is in particular true for analyses of rare immune and/or stem cell populations that are directly isolated from humans or animal models, and which are often characterized by multiple surface markers. To overcome these limitations, here we have developed proximity ligation imaging cytometry (PLIC), a protocol for proteomic analysis of rare cells...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142207/phosphorylation-dynamics-dominate-the-regulated-proteome-during-early-xenopus-development
#12
Elizabeth H Peuchen, Olivia F Cox, Liangliang Sun, Alex S Hebert, Joshua J Coon, Matthew M Champion, Norman J Dovichi, Paul W Huber
The earliest stages of animal development are largely controlled by changes in protein phosphorylation mediated by signaling pathways and cyclin-dependent kinases. In order to decipher these complex networks and to discover new aspects of regulation by this post-translational modification, we undertook an analysis of the X. laevis phosphoproteome at seven developmental stages beginning with stage VI oocytes and ending with two-cell embryos. Concurrent measurement of the proteome and phosphoproteome enabled measurement of phosphosite occupancy as a function of developmental stage...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142126/hpv-replication-regulation-by-acetylation-of-a-conserved-lysine-in-the-e2-protein
#13
Yanique Thomas, Elliot J Androphy
The Papillomavirus (PV) E2 protein is a sequence specific DNA binding protein that recruits cellular factors to its genome in infected epithelial cells. E2 also binds to and loads the viral E1 DNA helicase at the origin of replication. Post-translational modifications (PTMs) of PV E2 have been identified as potential regulators E2 functions. We recently reported lysine (K) 111 as a target of p300 acetylation in bovine (B)PV. The di-lysines at 111 and 112 are conserved in almost all papillomaviruses. We pursued a mutational approach to query the functional significance of lysine in human (H)PV E2...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29141220/phosphorylation-and-ubiquitination-regulate-protein-phosphatase-5-activity-and-its-prosurvival-role-in-kidney-cancer
#14
Natela Dushukyan, Diana M Dunn, Rebecca A Sager, Mark R Woodford, David R Loiselle, Michael Daneshvar, Alexander J Baker-Williams, John D Chisholm, Andrew W Truman, Cara K Vaughan, Timothy A Haystead, Gennady Bratslavsky, Dimitra Bourboulia, Mehdi Mollapour
The serine/threonine protein phosphatase 5 (PP5) regulates multiple cellular signaling networks. A number of cellular factors, including heat shock protein 90 (Hsp90), promote the activation of PP5. However, it is unclear whether post-translational modifications also influence PP5 phosphatase activity. Here, we show an "on/off switch" mechanism for PP5 regulation. The casein kinase 1δ (CK1δ) phosphorylates T362 in the catalytic domain of PP5, which activates and enhances phosphatase activity independent of Hsp90...
November 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/29140456/minimotif-miner-4-a-million-peptide-minimotifs-and-counting
#15
Kenneth F Lyon, Xingyu Cai, Richard J Young, Abdullah-Al Mamun, Sanguthevar Rajasekaran, Martin R Schiller
Minimotif Miner (MnM) is a database and web system for analyzing short functional peptide motifs, termed minimotifs. We present an update to MnM growing the database from ∼300 000 to >1 000 000 minimotif consensus sequences and instances. This growth comes largely from updating data from existing databases and annotation of articles with high-throughput approaches analyzing different types of post-translational modifications. Another update is mapping human proteins and their minimotifs to know human variants from the dbSNP, build 150...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138512/proteome-wide-identification-of-lysine-2-hydroxyisobutyrylation-reveals-conserved-and-novel-histone-modifications-in-physcomitrella-patens
#16
Zhiming Yu, Jun Ni, Wei Sheng, Zhikun Wang, Yuhuan Wu
Protein lysine 2-hydroxyisobutyrylation (Khib) is a newly identified post-translational modification found in animal and yeast cells. Previous research suggested that histone Khib is involved in male cell differentiation and plays a critical role in the regulation of chromatin functions in animals. However, information regarding protein Khib in plants is still limited. In this study, using a specific antibody and LC-MS/MS methods, we identified 11,976 Khib sites in 3,001 proteins in Physcomitrella patens. The bioinformatics analysis indicated that these Khib-modified proteins were involved in a wide range of molecular functions and cellular processes, and showed diverse subcellular localizations...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29137706/accurate-phosphorylation-site-localization-using-phospho-brackets
#17
Kaijie Xiao, Yun Shen, Shasha Li, Zhixin Tian
Phosphorylation is one of the most important and widely studied protein post-translational modifications. Tandem mass spectrometry using higher-energy collisional dissociation has evolved into a state-of-the-art analytical platform for both phosphorylation identification and site localization. Tens of thousands of phosphopeptides can now be routinely identified from a single shotgun proteomics study; site localization, however, is much more complicated and many challenges still exist. Here, we report our development of P-bracket using direct experimental evidence of phospho-containing site-determining product ions for accurate site localization without the need for additional FLR control...
December 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29137641/improving-e-coli-growth-performance-by-manipulating-small-rna-expression
#18
REVIEW
Alejandro Negrete, Joseph Shiloach
Efficient growth of E. coli, especially for production of recombinant proteins, has been a challenge for the biotechnological industry since the early 1970s. By employing multiple approaches, such as different media composition, various growth strategies and specific genetic manipulations, it is now possible to grow bacteria to concentrations exceeding 100 g/L and to achieve high concentrations of recombinant proteins. Although the growth conditions are carefully monitored and maintained, it is likely that during the growth process cells are exposed to periodic stress conditions, created by fluctuations in pH, dissolved oxygen, temperature, glucose, and salt concentration...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29137365/longitudinal-serum-metabolomics-evaluation-of-trastuzumab-and-everolimus-combination-as-pre-operative-treatment-for-her-2-positive-breast-cancer-patients
#19
Elodie Jobard, Olivier Trédan, Thomas Bachelot, Arnaud M Vigneron, Céline Mahier Aït-Oukhatar, Monica Arnedos, Maria Rios, Jacques Bonneterre, Véronique Diéras, Marta Jimenez, Jean-Louis Merlin, Mario Campone, Bénédicte Elena-Herrmann
The mammalian target of rapamycin complex 1 (mTORC1) is an attractive target for HER-2 positive breast cancer therapy because of its key role in protein translation regulation, cell growth and metabolism. We present here a metabolomic investigation exploring the impact of mTOR inhibition on serum metabolic profiles from patients with non-metastatic breast cancer overexpressing HER-2. Baseline, treatment-related and post-treatment serum samples were analyzed for 79 patients participating in the French clinical trial RADHER, in which randomized patients with HER-2 positive breast cancer received either trastuzumab alone (arm T) or a trastuzumab and everolimus combination (arm T+E)...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137327/regulation-of-fbxo4-mediated-icam-1-protein-stability-in-metastatic-breast-cancer
#20
Jae-Hyeok Kang, Mi-Young Choi, Yan-Hong Cui, Neha Kaushik, Nizam Uddin, Ki-Chun Yoo, Min-Jung Kim, Su-Jae Lee
Advanced or progressive cancers share common traits such as altered transcriptional modulation, genetic modification, and abnormal post-translational regulation. These processes influence protein stability and cellular activity. Intercellular adhesion molecule-1 (ICAM-1) is involved in the malignant progression of various human cancers, including breast, liver, renal, and pancreatic cancers, but protein stability has not been deal with in metastatic breast cancer. Additionally, the relevance of the stability maintenance of ICAM-1 protein remains obscure...
October 10, 2017: Oncotarget
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