Nature Chemical Biology Contents: July 2013 Volume 9 Number 7, pp 408 - 466

Advertisement Wondering where to publish your next paper?   Frontiers in Chemical Biology, a speciality section of Frontiers in Chemistry, offers a peer-reviewed and open access option to chemists, biologists and other researchers that develop and apply chemical tools to investigate biological systems and processes   Be a part of the future of research publication  TABLE OF CONTENTS July 2013 Volume 9, Issue 7 Research Highlights News and Views Articles Erratum Corrigenda Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Have you read this highly downloaded original article recently published in Cell Research?  Genome editing with RNA-guided Cas9 nuclease in Zebrafish embryos Nannan Chang, Changhong Sun, Lu Gao, Dan Zhu, Xiufei Xu, Xiaojun Zhu, Jing-Wei Xiong & Jianzhong Jeff Xi  To view articles in the top ten articles downloads, please visit: www.nature.com/cr/topten/index.html    Research Highlights Top Biosynthesis: Set me free | Cell biology: Viruses get an ESCRT | Microbiology: I'm beginning to see the light | Cell death: NonALKylating activity | tRNA Modifications: A structured answer | Protein folding: Retaining clients | Protein folding: Sweetening the deal | Microbiology: A lipid under stress News and Views Top Protein dynamics: Catch them if you can   pp410 - 411 Gianluigi Veglia doi:10.1038/nchembio.1258 NMR analysis of the conformational energy landscape of the catabolite activator protein suggests that allosteric inhibition can be achieved by blocking access to elusive high-energy states of proteins. See also: Article by Tzeng & Kalodimos Post-translational modifications: Panning for phosphohistidine   pp411 - 412 Matthew J Piggott and Paul V Attwood doi:10.1038/nchembio.1273 Elusive pan-phosphohistidine (pHis) antibodies have been generated using a hydrolytically stable triazolyl-phosphonate hapten, promising to substantially accelerate efforts to better understand the role of pHis in biology. See also: Article by Kee et al. Structural biology: FaPy lesions and DNA mutations   pp412 - 414 Kent S Gates doi:10.1038/nchembio.1274 Formamidopyrimidine residues are damaged purines that retain the same Watson-Crick hydrogen-bonding face found in the parent nucleobase, yet these lesions are mutagenic. Crystallographic evidence suggests molecular mechanisms by which these lesions 'mispair' to generate mutations during DNA replication. See also: Article by Gehrke et al. Signaling: Sifting at the ciliary base   pp414 - 415 Prachee Avasthi doi:10.1038/nchembio.1272 Transduction of extracellular signals by cilia requires regulated entry of pathway components. A new study uses chemical dimerization to induce diffusion and identifies size-dependent soluble diffusion rates consistent with a sieve-like barrier with 8-nm pore radii at the ciliary base. See also: Article by Lin et al. Chemical Biology JOBS of the week Postdoctoral Fellow / Research Scientist (Chemical Biology) Institute of Bioengineering and Nanotechnology (IBN) Biological / Chemical Oceanographer Australian Institue of Marine Science Chemical tools for studying the mechanism of ubiquitin transfer University of Dundee / MRC Phosphorylation and Ubiquitylation Unit PhD in Chemical Biology - Determination of Ubiquitin Signalling Complexes University of Dundee / MRC Phosphorylation and Ubiquitylation Unit Post Doctoral Associate Sanford-Burnham Medical Research Institute More Science jobs from Chemical Biology EVENT 2013 International Congress on Chemical, Biological and Environmental 8 August 2013 Indonesia More science events from Articles Top A pan-specific antibody for direct detection of protein histidine phosphorylation   pp416 - 421 Jung-Min Kee, Rob C Oslund, David H Perlman and Tom W Muir doi:10.1038/nchembio.1259 Studies of histidine phosphorylation have been limited owing to a lack of appropriate tools. The synthesis of a stable phosphohistidine mimic now leads to a pan antibody, enabling detection and further functional investigations of this little-known post-translational modification. Chemical compounds See also: News and Views by Piggott & Attwood A substrate radical intermediate in catalysis by the antibiotic resistance protein Cfr    pp422 - 427 Tyler L Grove, Jovan Livada, Erica L Schwalm, Michael T Green, Squire J Booker and Alexey Silakov doi:10.1038/nchembio.1251 The radical SAM enzyme Cfr catalyzes methylation of a ribosomal adenosine, causing broad antibiotic resistance. EPR and ENDOR techniques now provide direct evidence for the proposed enzymatic mechanism by detecting a central crosslinked intermediate in which a radical is located on the nucleotide. Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization   pp428 - 436 Hugo Lavoie, Neroshan Thevakumaran, Gwenaëlle Gavory, John J Li, Abbas Padeganeh, Sébastien Guiral, Jean Duchaine, Daniel Y L Mao, Michel Bouvier, Frank Sicheri and Marc Therrien doi:10.1038/nchembio.1257 ATP-competitive RAF kinase inhibitors stabilize a closed and rigid active conformation of the RAF kinase domain, which leads to RAF dimerization and allosteric activation of the inhibitor-free protomer. Chemically inducible diffusion trap at cilia reveals molecular sieve–like barrier   pp437 - 443 Yu-Chun Lin, Pawel Niewiadomski, Benjamin Lin, Hideki Nakamura, Siew Cheng Phua, John Jiao, Andre Levchenko, Takafumi Inoue, Rajat Rohatgi and Takanari Inoue doi:10.1038/nchembio.1252 Chemically inducible diffusion trap at cilia (CIDTc), a method to trap proteins in the cilia, was applied to study the kinetics of protein accumulation and reveal a molecular sieve at the ciliary base. CIDTc can also be applied to study signaling pathways in the cilia. See also: News and Views by Avasthi Mechanism-based corrector combination restores ΔF508-CFTR folding and function   pp444 - 454 Tsukasa Okiyoneda, Guido Veit, Johanna F Dekkers, Miklos Bagdany, Naoto Soya, Haijin Xu, Ariel Roldan, Alan S Verkman, Mark Kurth, Agnes Simon, Tamas Hegedus, Jeffrey M Beekman and Gergely L Lukacs doi:10.1038/nchembio.1253 Compounds that restore function to the cystic fibrosis–linked ΔF508 allele of CFTR can be classified on the basis of three corrector functions, representing different targets within the five domains of the channel protein. Combinations of individual compounds in the three classes can restore considerable function to the mutant channel. Unexpected non-Hoogsteen–based mutagenicity mechanism of FaPy-DNA lesions   pp455 - 461 Tim H Gehrke, Ulrike Lischke, Karola L Gasteiger, Sabine Schneider, Simone Arnold, Heiko C Müller, David S Stephenson, Hendrik Zipse and Thomas Carell doi:10.1038/nchembio.1254 Certain oxidative DNA lesions adopt altered conformational preferences that lead to mutations during replication. Biochemical and structural data reveal that for formamidopyrimidine lesions, tautomerization and altered base pair geometry in the DNA polymerase active site, rather than changes in glycosidic torsion angle, direct the mutagenicity of these lesions. Chemical compounds See also: News and Views by Gates Allosteric inhibition through suppression of transient conformational states   pp462 - 465 Shiou-Ru Tzeng and Charalampos G Kalodimos doi:10.1038/nchembio.1250 Advanced NMR studies of catabolite activator protein show that allosteric inhibitors can prevent conformational changes needed for a protein to bind its ligand, offering an explanation for why these inhibitors may not appear to cause any effect when monitored using static techniques. See also: News and Views by Veglia Erratum Top Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis   p466 Erik C Hett, Louise H Slater, Kevin G Mark, Tomohiko Kawate, Brian G Monks, Andrea Stutz, Eicke Latz and Deborah T Hung doi:10.1038/nchembio-0613-466a Corrigenda Top Allosteric peptides bind a caspase zymogen and mediate caspase tetramerization   p466 Karen Stanger, Micah Steffek, Lijuan Zhou, Christine D Pozniak, Clifford Quan, Yvonne Franke, Jeff Tom, Christine Tam, J Michael Elliott, Joseph W Lewcock, Yingnan Zhang, Jeremy Murray and Rami N Hannoush doi:10.1038/nchembio-0613-466b Protein dynamics: Catch them if you can   p466 Gianluigi Veglia doi:10.1038/nchembio-0613-466c Top Advertisement Special Issue and Web Focus on Total Syntheses of Antibiotics The March 2013 special issue of The Journal of Antibiotics on the Total Syntheses of Antibiotics features a review of the total syntheses of the 'big four' antibiotics, alongside a full listing of the 102 total syntheses and schematic diagrams of their chemical structures.  Take advantage of FREE access to select articles today!     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. 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