Mechanisms of Protein Translocation on DNA Are Differentially Responsive to Water Activity

December 5th, 2016 by Brigitte S. Naughton and Norbert O. Reich

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Biochemistry
DOI: 10.1021/acs.biochem.6b00872

Genome-wide chemical mapping of O-GlcNAcylated proteins in Drosophila melanogaster

December 5th, 2016 by Ta-Wei Liu

Nature Chemical Biology 13, 161 (2017). doi:10.1038/nchembio.2247

Authors: Ta-Wei Liu, Mike Myschyshyn, Donald A Sinclair, Samy Cecioni, Kevin Beja, Barry M Honda, Ryan D Morin & David J Vocadlo

  • Posted in Nat Chem Biol, Publications
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Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine

December 5th, 2016 by Monica Yun Liu

Nature Chemical Biology 13, 181 (2017). doi:10.1038/nchembio.2250

Authors: Monica Yun Liu, Hedieh Torabifard, Daniel J Crawford, Jamie E DeNizio, Xing-Jun Cao, Benjamin A Garcia, G Andrés Cisneros & Rahul M Kohli

  • Posted in Nat Chem Biol, Publications
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Quantitating drug-target engagement in single cells in vitro and in vivo

December 5th, 2016 by J Matthew Dubach

Nature Chemical Biology 13, 168 (2017). doi:10.1038/nchembio.2248

Authors: J Matthew Dubach, Eunha Kim, Katherine Yang, Michael Cuccarese, Randy J Giedt, Labros G Meimetis, Claudio Vinegoni & Ralph Weissleder

  • Posted in Nat Chem Biol, Publications
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A human microprotein that interacts with the mRNA decapping complex

December 5th, 2016 by Nadia G D'Lima

Nature Chemical Biology 13, 174 (2017). doi:10.1038/nchembio.2249

Authors: 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

Molecular Identification of D-Ribulokinase in Budding Yeast and Mammals [Enzymology]

December 1st, 2016 by Charandeep Singh, Enrico Glaab, Carole L. Linster

Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins are predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and of its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S. cerevisiae Ydr109c and human FGGY has remained unknown. Untargeted metabolomics analysis of an S. cerevisiae deletion mutant of YDR109C revealed ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared to a wild-type strain. In human HEK293 cells, ribulose could only be detected when ribitol was added to the cultivation medium and under this condition, FGGY silencing led to ribulose accumulation. Biochemical characterization of the recombinant purified Ydr109c and FGGY proteins showed a clear substrate preference of both kinases for D-ribulose over a range of other sugars and sugar derivatives tested, including L-ribulose. Detailed sequence and structural analyses of Ydr109c and FGGY as well as homologs thereof furthermore allowed the definition of a 5-residue D-ribulokinase signature motif (TCSLV). The physiological role of the herein identified eukaryotic D-ribulokinase remains unclear, but we speculate that S. cerevisiae Ydr109c and human FGGY could act as metabolite repair enzymes, serving to re-phosphorylate free D-ribulose generated by promiscuous phosphatases from D-ribulose-5-phosphate. In human cells, FGGY can additionally participate in ribitol metabolism.

Gephyrin-binding peptides visualize postsynaptic sites and modulate neurotransmission

November 28th, 2016 by Hans Michael Maric

Nature Chemical Biology 13, 153 (2017). doi:10.1038/nchembio.2246

Authors: Hans Michael Maric, Torben Johann Hausrat, Franziska Neubert, Nils Ole Dalby, Sören Doose, Markus Sauer, Matthias Kneussel & Kristian Strømgaard

  • Posted in Nat Chem Biol, Publications
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Activation and reduction of carbon dioxide by nitrogenase iron proteins

November 28th, 2016 by Johannes G Rebelein

Nature Chemical Biology 13, 147 (2017). doi:10.1038/nchembio.2245

Authors: 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.

  • Posted in Nat Chem Biol, Publications
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Ubiquitin utilizes an acidic surface patch to alter chromatin structure

November 21st, 2016 by Galia T Debelouchina

Nature Chemical Biology 13, 105 (2017). doi:10.1038/nchembio.2235

Authors: Galia T Debelouchina, Karola Gerecht & Tom W Muir

  • Posted in Nat Chem Biol, Publications
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A computationally engineered RAS rheostat reveals RAS–ERK signaling dynamics

November 21st, 2016 by John C Rose

Nature Chemical Biology 13, 119 (2017). doi:10.1038/nchembio.2244

Authors: 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

  • Posted in Nat Chem Biol, Publications
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