Nature Chemical Biology Contents: March 2016, Volume 12 No 3 pp 125 - 199

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Advertisement Two NO COST pilot projects to be awarded. Register for our webcast on Building Better Therapeutics with Metabolomics and be eligible to submit your abstract for 1 of 2 50 sample projects using metabolomics.  Register for the webcast free online.   TABLE OF CONTENTS March 2016 Volume 12, Issue 3 Research Highlights News and Views Perspective Brief Communication Articles Advertisement Nature Insight Frontiers in Biology  This year's Frontiers in Biology Insight features Reviews on the processes that underlie metastasis, the positive influence of inflammation on tissue repair, the role of endothelial cells in organ development, growth and regeneration, the endoplasmic reticulum stress response and its contribution to disease, and antibiotic resistance. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Open for Submissions A new open access, multi-and interdisciplinary journal dedicated to publishing the finest research on both microbial biofilms and microbiomes, the journal is now open for submissions. Explore the benefits of submitting your next research article.   Advertisement nature.com webcasts Join us for our upcoming webcast with live Q&A: COMBATING ANTIBIOTIC RESISTANCE Presented by BioPharma Dealmakers Date: Wednesday, March 9, 2016 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET REGISTER FOR FREE Sponsored by: Antabio, Cempra, Helperby, Motif Bio, Polyphor     Research Highlights Top Optogenetics: Follow the PIF | Target identification: Getting cholesterol out | Catalytic DNA: Ligating with lambda | RNA modification: Translating for growth News and Views Top RNA conformation: Lightening up invisible states   pp126 - 127 Yun-Xing Wang doi:10.1038/nchembio.2030 The versatility of RNA is achieved in part through its ability to adopt various shapes of structures. A new technology called X-ray scattering interferometry enables the detection of 'invisible' states by lighting up gold pairs tagged to RNA molecules. See also: Article by Shi et al. Translation: Ribosomes make sweeping arrests   pp127 - 128 Diego A Alonzo and T Martin Schmeing doi:10.1038/nchembio.2027 The arrest peptides that function with the macrolide antibiotic erythromycin stall translating ribosomes in the presence of the antibiotic, leading to remodeling of the downstream mRNA and enhancement of the translation of resistance genes. Current work suggests that small changes in the nascent peptide dictate the ability of ribosomes to respond to this and other small molecules. See also: Article by Gupta et al. Chemical Biology JOBS of the week Postdoctoral position in Chemical and Structural Biology of RNA The Scripps Research Institute Postdoctoral position in Chemical and Structural Biology of RNA The Scripps Research Institute Lecturer, Biology Ohio State University Postdoctoral Fellowship in Prostate Cancer and Cancer Metabolism Cleveland Clinic, Cleveland, OH Postdoctoral Research Associate in Microfluidics NYU Abu Dhabi More Science jobs from Chemical Biology EVENT Chemical Biology Year-End Symposium 25 May 2016 New York, USA More science events from Perspective Top Development and application of bond cleavage reactions in bioorthogonal chemistry   pp129 - 137 Jie Li and Peng R Chen doi:10.1038/nchembio.2024 Bioorthogonal chemistry approaches have traditionally focused on selective ligation reactions between compatible reactive groups. This Perspective highlights progress in developing bioorthogonal cleavage reactions for diverse applications in chemical biology. Brief Communication Top Addicting diverse bacteria to a noncanonical amino acid   pp138 - 140 Drew S Tack, Jared W Ellefson, Ross Thyer, Bo Wang, Jimmy Gollihar et al. doi:10.1038/nchembio.2002 Expansion of the genetic code to noncanonical amino acids (NCAAs) has been limited by the lack of evolutionary pressure for organismal dependence on the NCAA. Linking bacterial survival to an engineered β-lactamase that requires a non-natural tyrosine analog engenders diverse bacteria with a stable, expanded genetic code. Articles Top Protonation of a glutamate residue modulates the dynamics of the drug transporter EmrE   pp141 - 145 Anindita Gayen, Maureen Leninger and Nathaniel J Traaseth doi:10.1038/nchembio.1999 The protonation state of Glu14 within the drug transporter EmrE is able to influence the conformational dynamics of the protein and thereby bias the inward-open conformation to facilitate substrate efflux. The solution structural ensembles of RNA kink-turn motifs and their protein complexes   pp146 - 152 Xuesong Shi, Lin Huang, David M J Lilley, Pehr B Harbury and Daniel Herschlag doi:10.1038/nchembio.1997 XSI analysis of two RNA kink-turn motifs, KtA and KtB, in a range of solution concentrations and in the presence of the kink-turn protein partner L7Ae reveals a restricted conformational ensemble that is regulated by ions and protein binding. See also: News and Views by Wang Nascent peptide assists the ribosome in recognizing chemically distinct small molecules   pp153 - 158 Pulkit Gupta, Bo Liu, Dorota Klepacki, Vrinda Gupta, Klaus Schulten et al. doi:10.1038/nchembio.1998 Point mutations in nascent peptides that regulate in the macrolide antibiotic resistance genes ermC and ermB can tune the recognition of the antibiotics erythromycin and telithromycin that control ribosome stalling and gene activation. See also: News and Views by Alonzo & Schmeing Frequency and amplitude control of cortical oscillations by phosphoinositide waves   pp159 - 166 Ding Xiong, Shengping Xiao, Su Guo, Qingsong Lin, Fubito Nakatsu et al. doi:10.1038/nchembio.2000 Oscillations of actin, FBP17 and N-WASP are coupled to phase-shifted phosphoinositide (PI) turnover that is regulated by the lipid phosphatases SHIP1, synaptojanin 2 and PI 3-kinases. PI(4,5)P2 turnover regulates wave amplitude and PI(3,4)P2 acts as a pacemaker. A topological and conformational stability alphabet for multipass membrane proteins   pp167 - 173 Xiang Feng and Patrick Barth doi:10.1038/nchembio.2001 A scan of the protein structure database looking for interhelical contacts across transmembrane protein helix trimers finds six distinct structural and topological classes with unique sequence-3D contact motifs that could prove useful in future protein design initiatives. Small-molecule targeting of a diapophytoene desaturase inhibits S. aureus virulence   pp174 - 179 Feifei Chen, Hongxia Di, Youxin Wang, Qiao Cao, Bin Xu et al. doi:10.1038/nchembio.2003 The antifungal drug naftifine blocks carotenoid pigment biosynthesis in Staphylococcus aureus through inhibition of a biosynthetic enzyme of staphyloxanthin, disabling an important virulence mechanism and thus making the pathogen susceptible to host oxidant killing. Chemical compounds A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1   pp180 - 187 Jacob I Stuckey, Bradley M Dickson, Nancy Cheng, Yanli Liu, Jacqueline L Norris et al. doi:10.1038/nchembio.2007 Chromodomains in chromatin-associated proteins act as 'readers' of methylated lysines within histones. Structural and computational design led to the identification of UNC3866, a potent, cell-active peptide-based inhibitor of the methyllysine reading functions of CBX and CDY chromodomains. Chemical compounds A two-state activation mechanism controls the histone methyltransferase Suv39h1   pp188 - 193 Manuel M Muller, Beat Fierz, Lenka Bittova, Glen Liszczak and Tom W Muir doi:10.1038/nchembio.2008 Suv39h1 is a histone methyltransferase that methylates H3K9 residues in heterochromatic regions of the genome. An approach using semisynthetic chromatin reveals a mechanism for heterochromatin spreading in which H3K9 trimethylation anchors and activates Suv39h1 for modification of proximal lysines. A pyridoxal phosphate-dependent enzyme that oxidizes an unactivated carbon-carbon bond   pp194 - 199 Yi-Ling Du, Rahul Singh, Lona M Alkhalaf, Eugene Kuatsjah, Hai-Yan He et al. doi:10.1038/nchembio.2009 Pyridoxal 5-phosphate (PLP) is an essential coenzyme involved in diverse amino acid transformations. The discovery that Ind4 catalyzes the PLP-dependent oxidation of an unactivated carbon of L-arginine, as a part of the indolmycin biosynthetic pathway, expands the scope of reactions facilitated by PLP-dependent enzymes. Top 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. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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