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Nature Chemical Biology

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https://www.readbyqxmd.com/read/27918561/a-human-microprotein-that-interacts-with-the-mrna-decapping-complex
#1
Nadia G D'Lima, Jiao Ma, Lauren Winkler, Qian Chu, Ken H Loh, Elizabeth O Corpuz, Bogdan A Budnik, Jens Lykke-Andersen, Alan Saghatelian, Sarah A Slavoff
Proteomic detection of non-annotated microproteins indicates the translation of hundreds of small open reading frames (smORFs) in human cells, but whether these microproteins are functional or not is unknown. Here, we report the discovery and characterization of a 7-kDa human microprotein we named non-annotated P-body dissociating polypeptide (NoBody). NoBody interacts with mRNA decapping proteins, which remove the 5' cap from mRNAs to promote 5'-to-3' decay. Decapping proteins participate in mRNA turnover and nonsense-mediated decay (NMD)...
December 5, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27918560/genome-wide-chemical-mapping-of-o-glcnacylated-proteins-in-drosophila-melanogaster
#2
Ta-Wei Liu, Mike Myschyshyn, Donald A Sinclair, Samy Cecioni, Kevin Beja, Barry M Honda, Ryan D Morin, David J Vocadlo
N-Acetylglucosamine β-O-linked to nucleocytoplasmic proteins (O-GlcNAc) is implicated in the regulation of gene expression in organisms, from humans to Drosophila melanogaster. Within Drosophila, O-GlcNAc transferase (OGT) is one of the Polycomb group proteins (PcGs) that act through Polycomb group response elements (PREs) to silence homeotic (HOX) and other PcG target genes. Using Drosophila, we identify new O-GlcNAcylated PcG proteins and develop an antibody-free metabolic feeding approach to chemoselectively map genomic loci enriched in O-GlcNAc using next-generation sequencing...
December 5, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27918559/mutations-along-a-tet2-active-site-scaffold-stall-oxidation-at-5-hydroxymethylcytosine
#3
Monica Yun Liu, Hedieh Torabifard, Daniel J Crawford, Jamie E DeNizio, Xing-Jun Cao, Benjamin A Garcia, G Andrés Cisneros, Rahul M Kohli
Ten-eleven translocation (TET) enzymes catalyze stepwise oxidation of 5-methylcytosine (mC) to yield 5-hydroxymethylcytosine (hmC) and the rarer bases 5-formylcytosine (fC) and 5-carboxylcytosine (caC). Stepwise oxidation obscures how each individual base forms and functions in epigenetic regulation, and prompts the question of whether TET enzymes primarily serve to generate hmC or are adapted to produce fC and caC as well. By mutating a single, conserved active site residue in human TET2, Thr1372, we uncovered enzyme variants that permit oxidation to hmC but largely eliminate fC and caC...
December 5, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27918558/quantitating-drug-target-engagement-in-single-cells-in-vitro-and-in-vivo
#4
J Matthew Dubach, Eunha Kim, Katherine Yang, Michael Cuccarese, Randy J Giedt, Labros G Meimetis, Claudio Vinegoni, Ralph Weissleder
Quantitation of drug target engagement in single cells has proven to be difficult, often leaving unanswered questions in the drug development process. We found that intracellular target engagement of unlabeled new therapeutics can be quantitated using polarized microscopy combined with competitive binding of matched fluorescent companion imaging probes. We quantitated the dynamics of target engagement of covalent BTK inhibitors, as well as reversible PARP inhibitors, in populations of single cells using a single companion imaging probe for each target...
December 5, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27893705/gephyrin-binding-peptides-visualize-postsynaptic-sites-and-modulate-neurotransmission
#5
Hans Michael Maric, Torben Johann Hausrat, Franziska Neubert, Nils Ole Dalby, Sören Doose, Markus Sauer, Matthias Kneussel, Kristian Strømgaard
γ-Aminobutyric acid type A and glycine receptors are the major mediators of fast synaptic inhibition in the human central nervous system and are established drug targets. However, all drugs targeting these receptors bind to the extracellular ligand-binding domain of the receptors, which inherently is associated with perturbation of the basic physiological action. Here we pursue a fundamentally different approach, by instead targeting the intracellular receptor-gephyrin interaction. First, we defined the gephyrin peptide-binding consensus sequence, which facilitated the development of gephyrin super-binding peptides and later effective affinity probes for the isolation of native gephyrin...
November 28, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27893704/activation-and-reduction-of-carbon-dioxide-by-nitrogenase-iron-proteins
#6
Johannes G Rebelein, Martin T Stiebritz, Chi Chung Lee, Yilin Hu
The iron (Fe) proteins of molybdenum (Mo) and vanadium (V) nitrogenases mimic carbon monoxide (CO) dehydrogenase in catalyzing the interconversion between CO2 and CO under ambient conditions. Catalytic reduction of CO2 to CO is achieved in vitro and in vivo upon redox changes of the Fe-protein-associated [Fe4S4] clusters. These observations establish the Fe protein as a model for investigation of CO2 activation while suggesting its biotechnological adaptability for recycling the greenhouse gas into useful products...
November 28, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27870838/a-computationally-engineered-ras-rheostat-reveals-ras-erk-signaling-dynamics
#7
John C Rose, Po-Ssu Huang, Nathan D Camp, Jordan Ye, Andrew M Leidal, Inna Goreshnik, Bridget M Trevillian, Miles S Dickinson, Daniel Cunningham-Bryant, Jayanta Debnath, David Baker, Alejandro Wolf-Yadlin, Dustin J Maly
Synthetic protein switches controlled with user-defined inputs are powerful tools for studying and controlling dynamic cellular processes. To date, these approaches have relied primarily on intermolecular regulation. Here we report a computationally guided framework for engineering intramolecular regulation of protein function. We utilize this framework to develop chemically inducible activator of RAS (CIAR), a single-component RAS rheostat that directly activates endogenous RAS in response to a small molecule...
November 21, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27870837/ubiquitin-utilizes-an-acidic-surface-patch-to-alter-chromatin-structure
#8
Galia T Debelouchina, Karola Gerecht, Tom W Muir
Ubiquitylation of histone H2B, associated with gene activation, leads to chromatin decompaction through an unknown mechanism. We used a hydrogen-deuterium exchange strategy coupled with NMR spectroscopy to map the ubiquitin surface responsible for its structural effects on chromatin. Our studies revealed that a previously uncharacterized acidic patch on ubiquitin comprising residues Glu16 and Glu18 is essential for decompaction. These residues mediate promiscuous electrostatic interactions with the basic histone proteins, potentially positioning the ubiquitin moiety as a dynamic 'wedge' that prevents the intimate association of neighboring nucleosomes...
November 21, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27870836/the-rna-helicase-mtr4p-is-a-duplex-sensing-translocase
#9
Eric M Patrick, Sukanya Srinivasan, Eckhard Jankowsky, Matthew J Comstock
The conserved Saccharomyces cerevisiae Ski2-like RNA helicase Mtr4p plays essential roles in eukaryotic nuclear RNA processing. RNA helicase activity of Mtr4p is critical for biological functions of the enzyme, but the molecular basis for RNA unwinding is not understood. Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3'-to-5' translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps...
November 21, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27870835/full-antagonism-of-the-estrogen-receptor-without-a-prototypical-ligand-side-chain
#10
Sathish Srinivasan, Jerome C Nwachukwu, Nelson E Bruno, Venkatasubramanian Dharmarajan, Devrishi Goswami, Irida Kastrati, Scott Novick, Jason Nowak, Valerie Cavett, Hai-Bing Zhou, Nittaya Boonmuen, Yuechao Zhao, Jian Min, Jonna Frasor, Benita S Katzenellenbogen, Patrick R Griffin, John A Katzenellenbogen, Kendall W Nettles
Resistance to endocrine therapies remains a major clinical problem for the treatment of estrogen receptor-α (ERα)-positive breast cancer. On-target side effects limit therapeutic compliance and use for chemoprevention, highlighting an unmet need for new therapies. Here we present a full-antagonist ligand series lacking the prototypical ligand side chain that has been universally used to engender antagonism of ERα through poorly understood structural mechanisms. A series of crystal structures and phenotypic assays reveal a structure-based design strategy with separate design elements for antagonism and degradation of the receptor, and access to a structurally distinct space for further improvements in ligand design...
November 21, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27842070/acsl4-dictates-ferroptosis-sensitivity-by-shaping-cellular-lipid-composition
#11
Sebastian Doll, Bettina Proneth, Yulia Y Tyurina, Elena Panzilius, Sho Kobayashi, Irina Ingold, Martin Irmler, Johannes Beckers, Michaela Aichler, Axel Walch, Holger Prokisch, Dietrich Trümbach, Gaowei Mao, Feng Qu, Hulya Bayir, Joachim Füllekrug, Christina H Scheel, Wolfgang Wurst, Joel A Schick, Valerian E Kagan, José Pedro Friedmann Angeli, Marcus Conrad
Ferroptosis is a form of regulated necrotic cell death controlled by glutathione peroxidase 4 (GPX4). At present, mechanisms that could predict sensitivity and/or resistance and that may be exploited to modulate ferroptosis are needed. We applied two independent approaches-a genome-wide CRISPR-based genetic screen and microarray analysis of ferroptosis-resistant cell lines-to uncover acyl-CoA synthetase long-chain family member 4 (ACSL4) as an essential component for ferroptosis execution. Specifically, Gpx4-Acsl4 double-knockout cells showed marked resistance to ferroptosis...
November 14, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27842069/tunable-thermal-bioswitches-for-in-vivo-control-of-microbial-therapeutics
#12
Dan I Piraner, Mohamad H Abedi, Brittany A Moser, Audrey Lee-Gosselin, Mikhail G Shapiro
Temperature is a unique input signal that could be used by engineered microbial therapeutics to sense and respond to host conditions or spatially targeted external triggers such as focused ultrasound. To enable these possibilities, we present two families of tunable, orthogonal, temperature-dependent transcriptional repressors providing switch-like control of bacterial gene expression at thresholds spanning the biomedically relevant range of 32-46 °C. We integrate these molecular bioswitches into thermal logic circuits and demonstrate their utility in three in vivo microbial therapy scenarios, including spatially precise activation using focused ultrasound, modulation of activity in response to a host fever, and self-destruction after fecal elimination to prevent environmental escape...
November 14, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27842068/elucidation-of-gibberellin-biosynthesis-in-bacteria-reveals-convergent-evolution
#13
Ryan S Nett, Mariana Montanares, Ariana Marcassa, Xuan Lu, Raimund Nagel, Trevor C Charles, Peter Hedden, Maria Cecilia Rojas, Reuben J Peters
Gibberellins (GAs) are crucial phytohormones involved in many aspects of plant growth and development, including plant-microbe interactions, which has led to GA production by plant-associated fungi and bacteria as well. While the GA biosynthetic pathways in plants and fungi have been elucidated and found to have arisen independently through convergent evolution, little has been uncovered about GA biosynthesis in bacteria. Some nitrogen-fixing, symbiotic, legume-associated rhizobia, including Bradyrhizobium japonicum-the symbiont of soybean-and Sinorhizobium fredii-a broad-host-nodulating species-contain a putative GA biosynthetic operon, or gene cluster...
November 14, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27842067/ferroptosis-oxidized-pes-trigger-death
#14
Katharina D'Herde, Dmitri V Krysko
No abstract text is available yet for this article.
November 14, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27842066/oxidized-arachidonic-and-adrenic-pes-navigate-cells-to-ferroptosis
#15
Valerian E Kagan, Gaowei Mao, Feng Qu, Jose Pedro Friedmann Angeli, Sebastian Doll, Claudette St Croix, Haider Hussain Dar, Bing Liu, Vladimir A Tyurin, Vladimir B Ritov, Alexandr A Kapralov, Andrew A Amoscato, Jianfei Jiang, Tamil Anthonymuthu, Dariush Mohammadyani, Qin Yang, Bettina Proneth, Judith Klein-Seetharaman, Simon Watkins, Ivet Bahar, Joel Greenberger, Rama K Mallampalli, Brent R Stockwell, Yulia Y Tyurina, Marcus Conrad, Hülya Bayır
Enigmatic lipid peroxidation products have been claimed as the proximate executioners of ferroptosis-a specialized death program triggered by insufficiency of glutathione peroxidase 4 (GPX4). Using quantitative redox lipidomics, reverse genetics, bioinformatics and systems biology, we discovered that ferroptosis involves a highly organized oxygenation center, wherein oxidation in endoplasmic-reticulum-associated compartments occurs on only one class of phospholipids (phosphatidylethanolamines (PEs)) and is specific toward two fatty acyls-arachidonoyl (AA) and adrenoyl (AdA)...
November 14, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27820804/genetic-engineering-chemical-control-for-crispr-editing
#16
Isaac B Hilton, Charles A Gersbach
No abstract text is available yet for this article.
November 7, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27820802/inhibition-of-ras-function-through-targeting-an-allosteric-regulatory-site
#17
Russell Spencer-Smith, Akiko Koide, Yong Zhou, Raphael R Eguchi, Fern Sha, Priyanka Gajwani, Dianicha Santana, Ankit Gupta, Miranda Jacobs, Erika Herrero-Garcia, Jacqueline Cobbert, Hugo Lavoie, Matthew Smith, Thanashan Rajakulendran, Evan Dowdell, Mustafa Nazir Okur, Irina Dementieva, Frank Sicheri, Marc Therrien, John F Hancock, Mitsuhiko Ikura, Shohei Koide, John P O'Bryan
RAS GTPases are important mediators of oncogenesis in humans. However, pharmacological inhibition of RAS has proved challenging. Here we describe a functionally critical region, located outside the effector lobe of RAS, that can be targeted for inhibition. We developed NS1, a synthetic binding protein (monobody) that bound with high affinity to both GTP- and GDP-bound states of H-RAS and K-RAS but not N-RAS. NS1 potently inhibited growth factor signaling and oncogenic H-RAS- and K-RAS-mediated signaling and transformation but did not block oncogenic N-RAS, BRAF or MEK1...
November 7, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27820800/identification-of-g-quadruplexes-in-long-functional-rnas-using-7-deazaguanine-rna
#18
Carika Weldon, Isabelle Behm-Ansmant, Laurence H Hurley, Glenn A Burley, Christiane Branlant, Ian C Eperon, Cyril Dominguez
RNA G-quadruplex (G4) structures are thought to affect biological processes, including translation and pre-mRNA splicing, but it is not possible at present to demonstrate that they form naturally at specific sequences in long functional RNA molecules. We developed a new strategy, footprinting of long 7-deazaguanine-substituted RNAs (FOLDeR), that allows the formation of G4s to be confirmed in long RNAs and under functional conditions.
November 7, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27820798/dpp8-and-dpp9-inhibition-induces-pro-caspase-1-dependent-monocyte-and-macrophage-pyroptosis
#19
Marian C Okondo, Darren C Johnson, Ramya Sridharan, Eun Bin Go, Ashley J Chui, Mitchell S Wang, Sarah E Poplawski, Wengen Wu, Yuxin Liu, Jack H Lai, David G Sanford, Michael O Arciprete, Todd R Golub, William W Bachovchin, Daniel A Bachovchin
Val-boroPro (Talabostat, PT-100), a nonselective inhibitor of post-proline cleaving serine proteases, stimulates mammalian immune systems through an unknown mechanism of action. Despite this lack of mechanistic understanding, Val-boroPro has attracted substantial interest as a potential anticancer agent, reaching phase 3 trials in humans. Here we show that Val-boroPro stimulates the immune system by triggering a proinflammatory form of cell death in monocytes and macrophages known as pyroptosis. We demonstrate that the inhibition of two serine proteases, DPP8 and DPP9, activates the pro-protein form of caspase-1 independent of the inflammasome adaptor ASC...
November 7, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27820797/non-classical-transpeptidases-yield-insight-into-new-antibacterials
#20
Pankaj Kumar, Amit Kaushik, Evan P Lloyd, Shao-Gang Li, Rohini Mattoo, Nicole C Ammerman, Drew T Bell, Alexander L Perryman, Trevor A Zandi, Sean Ekins, Stephan L Ginell, Craig A Townsend, Joel S Freundlich, Gyanu Lamichhane
Bacterial survival requires an intact peptidoglycan layer, a three-dimensional exoskeleton that encapsulates the cytoplasmic membrane. Historically, the final steps of peptidoglycan synthesis are known to be carried out by D,D-transpeptidases, enzymes that are inhibited by the β-lactams, which constitute >50% of all antibacterials in clinical use. Here, we show that the carbapenem subclass of β-lactams are distinctly effective not only because they inhibit D,D-transpeptidases and are poor substrates for β-lactamases, but primarily because they also inhibit non-classical transpeptidases, namely the L,D-transpeptidases, which generate the majority of linkages in the peptidoglycan of mycobacteria...
November 7, 2016: Nature Chemical Biology
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