Nature Chemical Biology Contents: March 2018, Volume 14 No 3 pp 187 - 325

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Advertisement Discover the LOPAC®1280 small molecule library.  The power and performance of MilliporeSigma's Library of Pharmacologically Active Compounds is assured. 1,280 pharmacologically active compounds Ready-to-use DMSO stocks: less time-consuming sample preparation Highly pure compounds with full QC: re-supply as individual catalog items Learn More  TABLE OF CONTENTS March 2018 Volume 14, Issue 3 Editorial Commentaries Research Highlights News and Views Perspectives Reviews Brief Communication Articles Erratum Advertisement   Nature Catalysis is an online-only journal that publishes research, review and comment across all areas of catalysis.  EXPLORE THE LATEST ISSUE >>  Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Research 'lab health' survey 2018 The Nature Research's lab health survey aims to find out what makes a research group supportive, productive, and rigorous. The survey should take 10 to 15 minutes to complete and you'll have the chance to win a £100/$150 Amazon gift card. Your entries will be confidential and results will be featured in Nature.  Complete the survey today >>   Advertisement Naturejobs Career Guide China 2018 China's scientific landscape is shifting fast. Where can you fit in? Read the latest issue of our career guide to see what opportunities await you. Read more online    Editorial Top Altering form for function   p187 doi:10.1038/nchembio.2582 Elucidating the mechanisms by which biomolecules are chemically modified and how these alterations regulate biological pathways represents a leading frontier in chemical biology. Commentaries Top The ABCs of PTMs   pp188 - 192 Karl W Barber and Jesse Rinehart doi:10.1038/nchembio.2572 Post-translational modifications (PTMs) are ubiquitous in all forms of life and often modulate critical protein functions. Recent chemical and biological advances have finally enabled scientists to precisely modify proteins at physiologically relevant positions, ushering in a new era of protein studies. Covalent modifications of polysaccharides in mycobacteria   pp193 - 198 Shiva k Angala, Zuzana Palcekova, Juan M Belardinelli and Mary Jackson doi:10.1038/nchembio.2571 Mycobacteria produce carbohydrates of exceptional structures that are covalently modified by unique substituents, whose functional characterization could expand our understanding of how mycobacteria adapt to their environment. Research Highlights Top Lipids: Picturing palmitoylation | Viruses: Capsids under pressure | Glycosylation: Gluing on glycans | Ubiquitination: Trashing the CIA News and Views Top RNA structure: A LASER-focused view into cells   pp200 - 201 Philip C Bevilacqua and Sarah M Assmann doi:10.1038/nchembio.2570 RNA structure is irrevocably linked to function. A new method, termed 'LASER', utilizes a light-activated chemical probe to query RNA tertiary structure and illuminate RNA-protein interactions in the living cell. See also: Article by Feng et al. GPCR: Lock and key become flexible   pp201 - 202 Marc Baldus doi:10.1038/nchembio.2567 G-protein-coupled receptors (GPCRs) are critically involved in signal transduction. Structural views of several GPCRs have recently been obtained, but the structural principles determining subtype selectivity are still mostly elusive. Now, a combined solid-state NMR and molecular-modeling approach reveals how bradykinin GPCRs distinguish between closely related peptide ligands. See also: Article by Joedicke et al. Protein evolution: Hacking an enzyme   pp202 - 204 Kristoffer E Johansson and Jakob R Winther doi:10.1038/nchembio.2574 Early stages of protein evolution are inherently difficult to study. Genetic selection in Escherichia coli has now identified a life-sustaining de novo enzyme arising from a simple scaffold that is completely different from the native enzyme. See also: Brief Communication by Donnelly et al. Synthetic biology: Reframing cell therapy for cancer   pp204 - 205 Taylor B Dolberg, Patrick S Donahue and Joshua N Leonard doi:10.1038/nchembio.2573 Technologies for engineering immune cells to recognize features on cancer cells are transforming oncology. Synthetic biologists now expand this approach by conferring therapeutic functions to nonimmune cells and by programming cells to sense and respond to a new class of physiological cues. See also: Article by Chang et al. Nature Chemical Biology JOBS of the week Preclinical Scientist Imanova Limited Postdoctoral Fellow Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. Research Associate Heriot-Watt University Postdoctoral Fellow Joslin Diabetes Center/Harvard Medical School Postdoctoral Associate University of Minnesota - College of Pharmacy More Science jobs from Nature Chemical Biology EVENT ICBEE 2018 10th International Conference on Chemical, Biological and Environmental Engineering(ICBEE 2018) 27 - 29 September 2018 Berlin, Germany More science events from Perspectives Top How many human proteoforms are there?   pp206 - 214 Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi et al. doi:10.1038/nchembio.2576 Distinguishing RNA modifications from noise in epitranscriptome maps   pp215 - 225 Anya V Grozhik and Samie R Jaffrey doi:10.1038/nchembio.2546 Reviews Top Structural and evolutionary insights into ribosomal RNA methylation   pp226 - 235 Petr V Sergiev, Nikolay A Aleksashin, Anastasia A Chugunova, Yury S Polikanov and Olga A Dontsova doi:10.1038/nchembio.2569 Insights into the biogenesis, function, and regulation of ADP-ribosylation   pp236 - 243 Michael S Cohen and Paul Chang doi:10.1038/nchembio.2568 Features and regulation of non-enzymatic post-translational modifications   pp244 - 252 Robert Harmel and Dorothea Fiedler doi:10.1038/nchembio.2575 Brief Communication Top A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli   pp253 - 255 Ann E Donnelly, Grant S Murphy, Katherine M Digianantonio and Michael H Hecht doi:10.1038/nchembio.2550 A de novo-designed protein, Syn-F4, hydrolyzes the siderophore ferric enterobactin both in vitro and in Escherichia coli cells, enabling a bacterial strain lacking the essential natural enterobactin esterase to grow in iron-limited medium. See also: News and Views by Johansson & Winther Advertisement Do you have a career question?  The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud.  Listen today!   Articles Top Employing a biochemical protecting group for a sustainable indigo dyeing strategy   pp256 - 261 Tammy M Hsu, Ditte H Welner, Zachary N Russ, Bernardo Cervantes, Ramya L Prathuri et al. doi:10.1038/nchembio.2552 An environmentally friendly approach to indigo production is facilitated by the characterization of a plant indoxyl glucosyltransferase, which converts the unstable indoxyl precursor into indican by addition of a glucose protecting group. Na+-mimicking ligands stabilize the inactive state of leukotriene B4 receptor BLT1   pp262 - 269 Tetsuya Hori, Toshiaki Okuno, Kunio Hirata, Keitaro Yamashita, Yoshiaki Kawano et al. doi:10.1038/nchembio.2547 A structure of leukotriene B4 receptor BLT1 bound with a benzamidine-containing compound, BIIL260, reveals an inverse-agonist mechanism involving ligand binding in the sodium ion-centered water cluster adjacent to the conserved orthosteric site of class A GPCRs. Mechanism of intersubunit ketosynthase-dehydratase interaction in polyketide synthases   pp270 - 275 Matthew Jenner, Simone Kosol, Daniel Griffiths, Panward Prasongpholchai, Lucio Manzi et al. doi:10.1038/nchembio.2549 A combination of biochemical and structural techniques allows the characterization of a novel docking domain in polyketide synthases, which is structurally disordered and facilitates association of subunits at ketosynthase-dehydratase junctions. Light-activated chemical probing of nucleobase solvent accessibility inside cells   pp276 - 283 Chao Feng, Dalen Chan, Jojo Joseph, Mikko Muuronen, William H Coldren et al. doi:10.1038/nchembio.2548 A method called Light Activated Structural Examination of RNA (LASER) enables monitoring of the solvent accessibility of purine nucleobases and identifies rapid structural changes of cellular RNA-protein interactions and intracellular RNA structures. Chemical compounds See also: News and Views by Bevilacqua & Assmann The molecular basis of subtype selectivity of human kinin G-protein-coupled receptors   pp284 - 290 Lisa Joedicke, Jiafei Mao, Georg Kuenze, Christoph Reinhart, Tejaswi Kalavacherla et al. doi:10.1038/nchembio.2551 NMR to resolve the subtype specificity of two peptide ligands for human bradykinin receptors B1R and B2R shows different presentations of the peptide termini toward the receptor and interactions with nonconserved receptor binding-pocket residues. See also: News and Views by Baldus A whole-animal platform to advance a clinical kinase inhibitor into new disease space   pp291 - 298 Masahiro Sonoshita, Alex P Scopton, Peter M U Ung, Matthew A Murray, Lisa Silber et al. doi:10.1038/nchembio.2556 Combining Drosophila genetics with chemistry and computation led to the development of novel kinase inhibitors based on the RAF-targeting drug sorafenib that reveal the RET oncogene as an enhancer of drug action and improve the therapeutic window in medullary thyroid carcinoma models. Chemical compounds Chemical hijacking of auxin signaling with an engineered auxin-TIR1 pair   pp299 - 305 Naoyuki Uchida, Koji Takahashi, Rie Iwasaki, Ryotaro Yamada, Masahiko Yoshimura et al. doi:10.1038/nchembio.2555 A synthetic, orthogonal pair of the plant hormone auxin and its receptor TIR1 was engineered to hijack auxin signaling without interfering with the endogenous system. The synthetic system conclusively demonstrates the role for TIR1 in auxin-induced acid growth. Chemical compounds Lytic xylan oxidases from wood-decay fungi unlock biomass degradation   pp306 - 310 Marie Couturier, Simon Ladeveze, Gerlind Sulzenbacher, Luisa Ciano, Mathieu Fanuel et al. doi:10.1038/nchembio.2558 A new type of fungal lytic polysaccharide monooxygenase (LPMO) catalyzes the oxidative degradation of xylan components of cellulosic biomass and offers potential in wood biorefining. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity   pp311 - 316 Hao Yin, Chun-Qing Song, Sneha Suresh, Suet-Yan Kwan, Qiongqiong Wu et al. doi:10.1038/nchembio.2559 Partial substitution of CRISPR RNAs with DNA nucleotides retains CRISPR-Cas9 genome editing activity while enhancing efficiency and specificity within cells, suggesting that DNA-RNA hybrids may be economical reagents for targeted genome editing. Rewiring T-cell responses to soluble factors with chimeric antigen receptors   pp317 - 324 ZeNan L Chang, Michael H Lorenzini, Ximin Chen, Uyen Tran, Nathanael J Bangayan et al. doi:10.1038/nchembio.2565 Chimeric antigen receptor (CAR)-expressing T cells were engineered to recognize soluble protein ligands that, by inducing CAR dimerization, mechanically couple ligand binding and receptor signaling to produce immune effector molecules. See also: News and Views by Dolberg et al. Advertisement Animation on CRISPR: Gene editing and beyond The CRISPR-Cas9 system has revolutionised gene editing, but cutting DNA isn't all it can do. This Animation, from Nature Methods, explores where CRISPR might be headed next.  Watch the Animation >>  Produced with support from:  Dharmacon    Erratum Top Light-activated chemical probing of nucleobase solvent accessibility inside cells   p325 Chao Feng, Dalen Chan, Jojo Joseph, Mikko Muuronen, William H Coldren et al. doi:10.1038/nchembio0318-325 Top Advertisement nature.com webcasts Join us for our upcoming webcast with live Q&A:  FIGHTING INFECTIOUS DISEASES Presented by BioPharma Dealmakers Date: Tuesday, February 27, 2018 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET REGISTER FOR FREE Sponsored by: PaxVax, Inc., NovaBiotics Ltd, Wellcome    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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