Chemical biology articles within Nature Communications

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  • Article
    | Open Access

    The recognition of the mRNA codon by the tRNA anticodon is crucial for protein synthesis. Here the authors introduce non-standard nucleotides in bacterial and eukaryotic mRNA to reveal the minimal hydrogen bond requirement of codon-anticodon interaction for efficient and accurate translation.

    • Thomas Philipp Hoernes
    • , Klaus Faserl
    •  & Matthias David Erlacher

  • Article
    | Open Access

    Bacillus anthracis causes the infectious disease anthrax. Here, the authors synthesized deoxy glycosides that are effective against B. anthracis and related bacteria and found that these amphiphilic compounds kill bacteria via an unusual mechanism of action.

    • Catarina Dias
    • , João P. Pais
    •  & Amélia P. Rauter

  • Article
    | Open Access

    The construction of complex RNA-delivered genetic circuits in mammalian cells is challenging, though offers advantages over DNA circuits in clinical use. Here the authors construct a set of logic gates that respond to multiple miRNAs and demonstrate an apoptosis-regulatory AND gate.

    • Satoshi Matsuura
    • , Hiroki Ono
    •  & Hirohide Saito

  • Article
    | Open Access

    Diseases such as diabetes and Parkinson's manifest based on interactions between genes and environment. Here, the authors find among a panel of cell types that propargite, a common pesticide, induces pancreatic β-cell and dopamine neuron death and that loss of the gene GSTT1 confers hypersensitivity.

    • Ting Zhou
    • , Tae Wan Kim
    •  & Shuibing Chen

  • Article
    | Open Access

    Polyfluorinated hexopyranoses display unique physical, chemical and biological properties, however their stereoselective synthesis is highly challenging. Here, the authors report a synthetic approach based on the chemical manipulation of inexpensive levoglucosan to obtain heavily fluorinated monosaccharides stereoselectively.

    • Vincent Denavit
    • , Danny Lainé
    •  & Denis Giguère

  • Article
    | Open Access

    In vivo existence of guanine-rich four-stranded RNA structures (G4-RNAs) has been a matter of debate. Here the authors developed a protocol, G4RP-seq, to capture and identify transcriptome-wide G4-RNA, providing insights into the formation of transient G4-RNA in live human cells.

    • Sunny Y. Yang
    • , Pauline Lejault
    •  & David Monchaud

  • Article
    | Open Access

    The precise relationship between neurobehavioural effects and neurotransmitter effects of psychiatric drugs are not always understood. Here the authors develop a database documenting the neurotransmitter response in rats to 258 different neuropsychiatric drugs, and conclude that this neurotransmitter response does not, in general, reflect the current categorisation of those drugs.

    • Hamid R. Noori
    • , Lewis H. Mervin
    •  & Rainer Spanagel

  • Article
    | Open Access

    DNA phosphorothioation (PT-DNA) is a DNA backbone sulfur modification that is recognized by the type-IV restriction endonuclease ScoMcrA. Here the authors provide insights into sulfur recognition by solving the crystal structure of the PT-DNA bound sulfur-binding domain (SBD) from ScoMcrA and they further show that SBD homologs are widely spread among prokaryotes.

    • Guang Liu
    • , Wencheng Fu
    •  & Xinyi He

  • Article
    | Open Access

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a target for insulin sensitizing drugs. Here the authors combine NMR, X-ray crystallography and MD simulations and report a structural mechanism for eliciting PPARγ inverse agonism, where coactivator binding is inhibited and corepressor binding promoted, which causes PPARγ repression.

    • Richard Brust
    • , Jinsai Shang
    •  & Douglas J. Kojetin

  • Article
    | Open Access

    Guaianolides are pharmaceutically interesting molecules. Here, the authors isolate the enzyme kauniolide synthase from feverfew, show that it converts constunolide into a guaianolide via an unusual mechanism of action, and reconstruct the full kauniolide biosynthesis pathway in host organisms.

    • Qing Liu
    • , Arman Beyraghdar Kashkooli
    •  & Harro Bouwmeester

  • Article
    | Open Access

    Giant cell lesions of the jaw (GCLJ) are debilitating benign tumors of unclear origin. The authors identify driver recurrent somatic mutations in TRPV4, KRAS and FGFR1 and show they converge on aberrant activation of the MAPK pathway. Their findings extend the spectrum of TRPV4 channelopathies and provide rationale for targeted therapies at the bedside in GCLJ.

    • Carolina Cavalieri Gomes
    • , Tenzin Gayden
    •  & Nada Jabado

  • Article
    | Open Access

    The activity of several protein kinases is increased upon cellular production of reactive oxygen species, which can cause cysteine oxidation. Here the authors show that sulfenylation of specific cysteine residues within Src induce local structural changes that directly impact its activation.

    • David E. Heppner
    • , Christopher M. Dustin
    •  & Albert van der Vliet

  • Article
    | Open Access

    Activating mutations of the non-receptor protein tyrosine phosphatase SHP2 can cause cancer. Here the authors present the crystal structure of SHP2E76K, the most frequent cancer-associated SHP2 mutation, which adopts an open-state structure and show that the allosteric inhibitor SHP099 can revert SHP2E76K to its closed, autoinhibited conformation.

    • Jonathan R. LaRochelle
    • , Michelle Fodor
    •  & Stephen C. Blacklow

  • Article
    | Open Access

    Myoglobin bound to carbon monoxide undergoes an ultrafast light-induced reaction, which ends up in a photolyzed carbon monoxide and a spin transition of the iron center. Here, the authors employ quantum wavepacket dynamics to show that photolysis precedes the spin transition, a mechanism dominated by strong electron-nuclear couplings.

    • Konstantin Falahati
    • , Hiroyuki Tamura
    •  & Miquel Huix-Rotllant

  • Article
    | Open Access

    The hexahydropyrrolo[2, 3-b]indole (HPI) framework is found in many natural products. Here, the authors discover a P450 enzyme and develop a whole-cell biocatalysis system that produces the HPI naseseazine C (NAS-C) and 30 NAS-C analogs, several of which show neuroprotective properties.

    • Wenya Tian
    • , Chenghai Sun
    •  & Xudong Qu

  • Article
    | Open Access

    Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (NDD) and a NDD-CDD complex and derive a set of recognition rules for DD interactions.

    • Carolin Hacker
    • , Xiaofeng Cai
    •  & Jens Wöhnert

  • Article
    | Open Access

    Ischemic reperfusion or nutrient deprivation that produces reactive oxygen species can lead to a loss of muscle contractile function. Here the authors show that glutathionylation of the lysine methyltransferase SMYD2 contributes to degradation or disassembly of sarcomeres.

    • Dhanushka N. P. Munkanatta Godage
    • , Garrett C. VanHecke
    •  & Young-Hoon Ahn

  • Article
    | Open Access

    Targeting noncoding nucleic acids with small molecules represents an important and significant challenge in chemical biology and drug discovery. Here the authors characterize DC-34, a small molecule that exhibits selective binding to specific G4 structures, and provide a structural basis for its selectivity

    • David R. Calabrese
    • , Xiang Chen
    •  & John S. Schneekloth Jr.

  • Article
    | Open Access

    Membrane bilayers are made up of a myriad of different lipids that affect membrane proteins, but identifying those specific lipid requirements remains a challenge. Here authors present an engineered thermal-shift screen which reveals specific lipid preferences of eukaryotic and prokaryotic membrane proteins.

    • Emmanuel Nji
    • , Yurie Chatzikyriakidou
    •  & David Drew

  • Article
    | Open Access

    Secondary transporters catalyse substrate translocation across the cell membrane but the role of lipids during the transport cycle remains unclear. Here authors used hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations to understand how lipids regulate the conformational dynamics of secondary transporters.

    • Chloe Martens
    • , Mrinal Shekhar
    •  & Argyris Politis

  • Article
    | Open Access

    Higher order coiled coils with five or more helices can form α-helical barrels. Here the authors show that placing β-branched aliphatic residues along the lumen yields stable and open α-helical barrels, which is of interest for the rational design of functional proteins; whereas, the absence of β-branched side chains leads to unusual low-symmetry α-helical bundles.

    • Guto G. Rhys
    • , Christopher W. Wood
    •  & Derek N. Woolfson

  • Article
    | Open Access

    Diketopiperazine derivatives are bioactive molecules with scaffold formed by the condensation of two amino acids. Here, Yao et al. mine the genomes of Streptomyces strains and identify new biosynthetic machinery for drimentines biosynthesis, which includes cyclodipeptide synthase, prenyltransferase, and terpene cyclase.

    • Tingting Yao
    • , Jing Liu
    •  & Wenli Li

  • Article
    | Open Access

    Designing split protein approaches is time consuming and often results in high background activity due to spontaneous assembly. Here the authors present an automated approach which uses a split energy scoring function to identify optimal protein split sites and reduces spontaneous assembly.

    • Onur Dagliyan
    • , Andrey Krokhotin
    •  & Nikolay V. Dokholyan

  • Article
    | Open Access

    New natural products can be identified via mass spectrometry by excluding all known ones from the analysis, a process called dereplication. Here, the authors extend a previously published dereplication algorithm to different classes of secondary metabolites.

    • Hosein Mohimani
    • , Alexey Gurevich
    •  & Pavel A. Pevzner

  • Article
    | Open Access

    Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is a common bioconjugation technique; however oxidative degradation and residual copper may limit its use. Here, the authors show that ppm levels of Cu, generated in situ by solvent-mediated pipe erosion in flow, catalyze the CuAAC reaction with no product degradation.

    • Marine Z. C. Hatit
    • , Linus F. Reichenbach
    •  & Allan J. B. Watson

  • Article
    | Open Access

    Assimilating the abundant one-carbon compounds by an industrially-relevant microorganism can broaden the substrate range and achieve reactions that are difficult for chemical process. Here the authors show a modified serine cycle can convert methanol and CO2 to two-carbon compounds in an engineered E. coli strain.

    • Hong Yu
    •  & James C. Liao

  • Article
    | Open Access

    The bacterial diterpene synthase CotB2 catalyses the cyclisation of geranylgeranyl diphosphate to cyclooctat-9-en7-ol. Here the authors present various CotB2 structures including a trapped abrupt reaction product that were used for molecular dynamic simulations and allowed them to model all intermediates along the reaction cascade.

    • Ronja Driller
    • , Sophie Janke
    •  & Bernhard Loll

  • Article
    | Open Access

    The monoamine oxidase family member LkcE is an enzyme from the lankacidin polyketide biosynthetic pathway, where it catalyzes an amide oxidation followed by an intramolecular Mannich reaction, yielding the polyketide macrocycle. Here the authors characterize LkcE and present several of its crystal structures, which explains the unusual dual activity of LkcE.

    • Jonathan Dorival
    • , Fanny Risser
    •  & Kira J. Weissman

  • Article
    | Open Access

    Strobilurins are fungal metabolites that inspired the creation of β-methoxyacrylate agricultural fungicides. Here, Nofiani et al. identify the strobilurin biosynthesis gene cluster, encoding a polyketide synthase as well as an FAD-dependent oxygenase for an oxidative rearrangement leading to β-methoxyacrylate formation.

    • Risa Nofiani
    • , Kate de Mattos-Shipley
    •  & Russell J. Cox

  • Article
    | Open Access

    Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.

    • Martin Baumdick
    • , Márton Gelléri
    •  & Philippe I. H. Bastiaens

  • Article
    | Open Access

    HIV envelope (Env) is a potential vaccine antigen and its N-glycans are part of the epitope of broadly neutralizing antibodies. Here, the authors show that glycosylation of Env from infectious virus closely matches Env from recombinant membrane-bound trimers, while it differs significantly from recombinant soluble, cleaved Env trimers.

    • Liwei Cao
    • , Matthias Pauthner
    •  & James C. Paulson

  • Article
    | Open Access

    The natural products fosfazinomycin A and kinamycin D are structurally distinct except for a nitrogen-nitrogen (N-N) bond. Here, the authors show that fosfazinomycin and kinamycin share a common pathway for N-N bond formation that is different from pathways found for other natural products.

    • Kwo-Kwang A. Wang
    • , Tai L. Ng
    •  & Wilfred A. van der Donk

  • Article
    | Open Access

    The phytohormone JA-Ile can promote plant resistance against herbivores and fungal pathogens but also inhibits growth, limiting its potential use in agriculture. Here, the authors design a stereoisomer of JA-Ile analog and demonstrate that it can promote defense while having minimal impact on growth.

    • Yousuke Takaoka
    • , Mana Iwahashi
    •  & Minoru Ueda

  • Article
    | Open Access

    Bioluminescence resonance energy transfer (BRET) has been mostly employed in imaging applications. Here the authors use BRET to activate a ruthenium-based photocatalyst and perform a bioorthogonal chemical reaction, which can be used to uncage small molecule drugs in a cellular context.

    • Eric Lindberg
    • , Simona Angerani
    •  & Nicolas Winssinger

  • Article
    | Open Access

    Histone marks regulate chromatin structure and function. Here the authors identify and characterize lysine benzoylation, a histone mark that can be modulated by sodium benzoate, a widely used chemical food preservative, associated with specific regulation of gene expression.

    • He Huang
    • , Di Zhang
    •  & Yingming Zhao

  • Article
    | Open Access

    While drugs can interact in both target and off-target cell types, more favorable interaction in the target cell may nevertheless allow for a therapeutic window. Here, the authors show, using two yeast species as a model, that differential drug interactions indeed adjust the selective window.

    • Zohar B. Weinstein
    • , Nurdan Kuru
    •  & Murat Cokol

  • Article
    | Open Access

    His-tagged proteins can undergo N-terminal acylation as an undesired side-reaction. Here, the authors utilize this to develop a method for highly selective acylation and further modification of peptides and proteins using an optimized His sequence and 4-methoxyphenyl esters as acyl donors.

    • Manuel C. Martos-Maldonado
    • , Christian T. Hjuler
    •  & Knud J. Jensen

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