Decoding cyclase-dependent assembly of hapalindole and fischerindole alkaloids

March 13th, 2017 by Shasha Li

Nature Chemical Biology 13, 467 (2017). doi:10.1038/nchembio.2327

Authors: Shasha Li, Andrew N Lowell, Sean A Newmister, Fengan Yu, Robert M Williams & David H Sherman

The formation of C–C bonds in an enantioselective fashion to create complex polycyclic scaffolds in the hapalindole- and fischerindole- type alkaloids from Stigonematales cyanobacteria represents a compelling and urgent challenge in adapting microbial biosynthesis as a catalytic platform in drug development. Here we determine the biochemical basis for tri- and tetracyclic core formation in these secondary metabolites, involving a new class of cyclases that catalyze a complex cyclization cascade.

  • Posted in Nat Chem Biol, Publications
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In silico design of novel probes for the atypical opioid receptor MRGPRX2

March 13th, 2017 by Katherine Lansu

Nature Chemical Biology 13, 529 (2017). doi:10.1038/nchembio.2334

Authors: Katherine Lansu, Joel Karpiak, Jing Liu, Xi-Ping Huang, John D McCorvy, Wesley K Kroeze, Tao Che, Hiroshi Nagase, Frank I Carroll, Jian Jin, Brian K Shoichet & Bryan L Roth

  • Posted in Nat Chem Biol, Publications
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The Rrp4–exosome complex recruits and channels substrate RNA by a unique mechanism

March 13th, 2017 by Milos A Cvetkovic

Nature Chemical Biology 13, 522 (2017). doi:10.1038/nchembio.2328

Authors: Milos A Cvetkovic, Jan Philip Wurm, Maxime J Audin, Stefan Schütz & Remco Sprangers

  • Posted in Nat Chem Biol, Publications
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Two alternative binding mechanisms connect the protein translocation Sec71/Sec72 complex with heat shock proteins [Protein Structure and Folding]

March 12th, 2017 by Arati Tripathi, Elisabet C Mandon, Reid Gilmore, Tom A Rapoport

The biosynthesis of many eukaryotic proteins requires accurate targeting to and translocation across the endoplasmic reticulum (ER) membrane. Post-translational protein translocation in yeast requires both the Sec61 translocation channel, and a complex of four additional proteins: Sec63, Sec62, Sec71, and Sec72. The structure and function of these proteins are largely unknown. This pathway also requires the cytosolic Hsp70 protein Ssa1, but whether Ssa1 associates with the translocation machinery to target protein substrates to the membrane is unclear. Here, we use a combined structural and biochemical approach to explore the role of Sec71/Sec72 subcomplex in post-translational protein translocation. To this end, we report a crystal structure of the Sec71/Sec72 complex, which revealed that Sec72 contains a tetratricopeptide repeat (TPR) domain that is anchored to the ER membrane by Sec71. We also determined the crystal structure of this TPR domain with a C-terminal peptide derived from Ssa1, which suggests how Sec72 interacts with full-length Ssa1. Surprisingly, Ssb1, a cytoplasmic Hsp70 that binds ribosome- associated nascent polypeptide chains also binds to the TPR domain of Sec72, even though it lacks the TPR-binding C-terminal residues of Ssa1. We demonstrate that Ssb1 binds through its ATPase domain to the TPR domain, an interaction that leads to inhibition of nucleotide exchange. Taken together, our results suggest that translocation substrates can be recruited to the Sec71/72 complex either post-translationally through Ssa1 or co-translationally through Ssb1.
  • Posted in Journal of Biological Chemistry, Publications
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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

TOC Graphic

Biochemistry
DOI: 10.1021/acs.biochem.6b01063

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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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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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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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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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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