Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes

March 7th, 2017 by Damien Jefferies, Pin-Chia Hsu and Syma Khalid

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Biochemistry
DOI: 10.1021/acs.biochem.6b01063

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

March 6th, 2017 by Andrew M Intlekofer

Nature Chemical Biology 13, 494 (2017). doi:10.1038/nchembio.2307

Authors: Andrew M Intlekofer, Bo Wang, Hui Liu, Hardik Shah, Carlos Carmona-Fontaine, Ariën S Rustenburg, Salah Salah, M R Gunner, John D Chodera, Justin R Cross & Craig B Thompson

  • Posted in Nat Chem Biol, Publications
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The structure of a nucleolytic ribozyme that employs a catalytic metal ion

March 6th, 2017 by Yijin Liu

Nature Chemical Biology 13, 508 (2017). doi:10.1038/nchembio.2333

Authors: Yijin Liu, Timothy J Wilson & David M J Lilley

  • Posted in Nat Chem Biol, Publications
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Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis

March 6th, 2017 by Sarah A Boswell

Nature Chemical Biology 13, 501 (2017). doi:10.1038/nchembio.2317

Authors: Sarah A Boswell, Andrew Snavely, Heather M Landry, L Stirling Churchman, Jesse M Gray & Michael Springer

  • Posted in Nat Chem Biol, Publications
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A New General Method for Simultaneous Fitting of Temperature- and Concentration-Dependence of Reaction Rates Yields Kinetic and Thermodynamic Parameters for HIV Reverse Transcriptase Specificity [DNA and Chromosomes]

March 2nd, 2017 by An Li, Jessica L. Ziehr, Kenneth A. Johnson

Recent studies have demonstrated the dominant role of induced-fit in enzyme specificity of HIV reverse transcriptase and many other enzymes. However, relevant thermodynamic parameters are lacking and equilibrium thermodynamic methods are of no avail because the key parameters can only determined by kinetic measurement. By modifying KinTek Explorer software, we present a new general method for globally fitting data collected over a range of substrate concentrations and temperatures and apply it to HIV reverse transcriptase. Fluorescence stopped-flow methods were used to record the kinetics of enzyme conformational changes that monitor nucleotide binding and incorporation. The nucleotide concentration dependence was measured at temperatures ranging from 5 to 37C and the raw data were fit globally to derive a single set of rate constants at 37C and a set of activation enthalpy terms to account for the kinetics at all other temperatures. This comprehensive analysis afforded thermodynamic parameters for nucleotide binding (Kd, ΔG, ΔH, ΔS at 37C), and kinetic parameters for enzyme conformational changes and chemistry (rate constants and activation enthalpy). Comparisons between wild-type enzyme and a mutant resistant to nucleoside analogs used to treat HIV infections reveal that the ground state binding is weaker and the activation enthalpy for the conformational change step is significantly larger for the mutant. Further studies to explore the structural underpinnings of the observed thermodynamics and kinetics of the conformational change step may help to design better analogs to treat HIV infections and other diseases. Our new method is generally applicable to enzyme and chemical kinetics.
  • Posted in Journal of Biological Chemistry, Publications
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Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11

February 28th, 2017 by Jing Li

Nature Chemical Biology 13, 486 (2017). doi:10.1038/nchembio.2326

Authors: Jing Li, Tanya Yakushi, Francesco Parlati, Andrew L Mackinnon, Christian Perez, Yuyong Ma, Kyle P Carter, Sharon Colayco, Gavin Magnuson, Brock Brown, Kevin Nguyen, Stefan Vasile, Eigo Suyama, Layton H Smith, Eduard Sergienko, Anthony B Pinkerton, Thomas D Y Chung, Amy E Palmer, Ian Pass, Sonja Hess, Seth M Cohen & Raymond J Deshaies

  • Posted in Nat Chem Biol, Publications
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A fully automated flow-based approach for accelerated peptide synthesis

February 28th, 2017 by Alexander J Mijalis

Nature Chemical Biology 13, 464 (2017). doi:10.1038/nchembio.2318

Authors: Alexander J Mijalis, Dale A Thomas, Mark D Simon, Andrea Adamo, Ryan Beaumont, Klavs F Jensen & Bradley L Pentelute

Here we report a fully automated, flow-based approach to solid-phase polypeptide synthesis, with amide bond formation in 7 seconds and total synthesis times of 40 seconds per amino acid residue. Crude peptide purities and isolated yields were comparable to those for standard-batch solid-phase peptide synthesis. At full capacity, this approach can yield tens of thousands of individual 30-mer peptides per year.

  • Posted in Nat Chem Biol, Publications
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A new genome-mining tool redefines the lasso peptide biosynthetic landscape

February 28th, 2017 by Jonathan I Tietz

Nature Chemical Biology 13, 470 (2017). doi:10.1038/nchembio.2319

Authors: Jonathan I Tietz, Christopher J Schwalen, Parth S Patel, Tucker Maxson, Patricia M Blair, Hua-Chia Tai, Uzma I Zakai & Douglas A Mitchell

  • Posted in Nat Chem Biol, Publications
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The Arabidopsis O-fucosyltransferase SPINDLY activates nuclear growth repressor DELLA

February 28th, 2017 by Rodolfo Zentella

Nature Chemical Biology 13, 479 (2017). doi:10.1038/nchembio.2320

Authors: Rodolfo Zentella, Ning Sui, Benjamin Barnhill, Wen-Ping Hsieh, Jianhong Hu, Jeffrey Shabanowitz, Michael Boyce, Neil E Olszewski, Pei Zhou, Donald F Hunt & Tai-ping Sun

  • Posted in Nat Chem Biol, Publications
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Synthetic Riboswitches: From Plug and Pray toward Plug and Play

February 24th, 2017 by Maja Etzel and Mario Mörl

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Biochemistry
DOI: 10.1021/acs.biochem.6b01218