Chemical biology articles within Nature Communications

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  • Article
    | Open Access

    Amine dehydrogenases (AmDHs) catalyse the conversion of ketones into amines. Here, the authors created AmDH variants, the best of which showing a substrate-dependent stereo-switchable selectivity, affording either S- or R-configured amine products with up to >99.9% enantiomeric excess.

    • Vasilis Tseliou
    • , Tanja Knaus
    •  & Francesco G. Mutti

  • Article
    | Open Access

    Tropane alkaloids (TAs) are a group of phytochemicals that are used to treat neurological disorders. Here, the authors engineer baker’s yeast to produce tropine, a key intermediate in the biosynthetic pathway of TAs, and cinnamoyltropine, a non-canonical TA, from simple carbon and nitrogen sources.

    • Prashanth Srinivasan
    •  & Christina D. Smolke

  • Article
    | Open Access

    Picornaviruses use modular RNA domains in their internal ribosome entry sites (IRESs) for translation through non-canonical, cap-independent mechanisms. Here the authors report the crystal structure of domain V from the IRES of hepatitis A virus (HAV) ssRNA genome, suggesting that the functional homology among different types of picornaviral IRESs is structure-based.

    • Deepak Koirala
    • , Yaming Shao
    •  & Joseph A. Piccirilli

  • Article
    | Open Access

    Microalbuminuria, a clinical marker associated with cancer and hypertension, defined by low albumin levels in the urine, is normally detected by immunoassay. Herein, a nanosensor paint was developed using a polymer to mimic fatty acid binding to albumin, transduced by carbon nanotube fluorescence.

    • Januka Budhathoki-Uprety
    • , Janki Shah
    •  & Daniel A. Heller

  • Article
    | Open Access

    Autophagy mediated by the conjugation pathway for ubiquitin-like proteins plays a key role in controlling homeostasis in eukaryotic cells. Here the authors provide a molecular basis for allosteric activation of the E2 ligase Atg3, uncovering the mechanism underlying Atg8 lipidation and a novel mechanism regulating E1-E2-E3-mediated ubiquitin-like protein conjugation.

    • Yumei Zheng
    • , Yu Qiu
    •  & Brenda A. Schulman

  • Article
    | Open Access

    It is thought that fungi protect themselves from predators by the production of toxic compounds. Here, Xu et al. show that a wide range of animal predators avoid feeding on Fusarium fungi, and this depends on fungal production of a bis-naphthopyrone pigment that is not toxic to the predators.

    • Yang Xu
    • , Maria Vinas
    •  & Petr Karlovsky

  • Article
    | Open Access

    The mechanism of iron-sulfur (Fe-S) cluster biosynthesis is not fully understood. Here, the authors develop a physiologically relevant in vitro model of Fe-S cluster assembly, allowing them to elucidate the sequence of Fe-S cluster synthesis along with the respective roles of ferredoxin-2 and frataxin.

    • Sylvain Gervason
    • , Djabir Larkem
    •  & Benoit D’Autréaux

  • Article
    | Open Access

    Targeted protein degradation (TPD) is a promising strategy for drug development. In this proof-of-concept study, the authors use telaprevir, which binds hepatitis C virus (HCV) NS3/4A protease, to target the protease for protein degradation, and show inhibition of wildtype as well as drug resistant HCV.

    • Mélissanne de Wispelaere
    • , Guangyan Du
    •  & Priscilla L. Yang

  • Article
    | Open Access

    The antimicrobial β-lactone obafluorin is produced by a Nonribosomal Peptide Synthetase (NRPS). Here the authors present the crystal structure of the obafluorin NRPS and develop a reconstitution assay that allows them to analyse product formation from obafluorin NRPS mutants and alternate substrates.

    • Dale F. Kreitler
    • , Erin M. Gemmell
    •  & Andrew M. Gulick

  • Article
    | Open Access

    C19 hydroxylation is a unique feature of some bioactive steroids. Here, the authors developed a direct C19 hydroxylation approach to scalably access 19-OH-cortexolone in the host T. cucumeris and then converted the product into various pharmaceutically useful products via chemical synthesis.

    • Junlin Wang
    • , Yanan Zhang
    •  & Qianghui Zhou

  • Article
    | Open Access

    Transfer RNA (tRNA) is regulated by RNA modifications. Here the authors employ time-resolved NMR to monitor modifications of yeast tRNAPhe in cellular extracts, revealing a sequential order and cross-talk between modifications.

    • Pierre Barraud
    • , Alexandre Gato
    •  & Carine Tisné

  • Article
    | Open Access

    Allosteric GPCR modulators can achieve exquisite subtype selectivity, but the underlying mechanism is unclear. Using molecular dynamics simulations, the authors here identify a previously undetected dynamic pocket in muscarinic GPCRs that is critical for subtype selectivity of allosteric modulators.

    • Scott A. Hollingsworth
    • , Brendan Kelly
    •  & Ron O. Dror

  • Article
    | Open Access

    Ribonucleotide reductase (RNR) catalyzes the de novo synthesis of deoxyribonucleoside diphosphates to provide dNTP precursors for DNA synthesis. Here the authors show that the availability of dNTPs, DNA replication, and cellular proliferation, are modulated by acetylation and deacetylation of RRM2 by KAT7 and Sirt2 respectively.

    • Guo Chen
    • , Yin Luo
    •  & Xingming Deng

  • Article
    | Open Access

    The inner centromere protein (INCENP) activates Aurora kinase B (AURKB) and Aurora kinase C. Here the authors provide insights into the activation mechanism of AURKB/C by determining the crystal structure of fully active phosphorylated human AURKC bound to the phosphorylated C-terminal IN-box section of human INCENP.

    • Kamal R. Abdul Azeez
    • , Sneha Chatterjee
    •  & Jonathan M. Elkins

  • Article
    | Open Access

    Core regulatory transcription factors are usually regulated by cell-type specific super enhancers (SEs). Here, the authors screen for chemical probes able to distinguish between SE-driven and promoter-driven transcription and find that histone deacetylases are selectively required for core regulatory transcription.

    • Berkley E. Gryder
    • , Lei Wu
    •  & Javed Khan

  • Article
    | Open Access

    Bats possess an extended lifespan compared to most mammals of their size, and have a low cancer incidence. Here the authors show that several bat species exhibit resistance to genotoxic agents that is in part attributable to high expression of the ABCB1 transporter.

    • Javier Koh
    • , Yoko Itahana
    •  & Koji Itahana

  • Article
    | Open Access

    Monitoring protein-protein interactions via bimolecular fluorescence complementation is often limited by the slow kinetics and irreversibility of the complementation. Here the authors introduce a fluorescent reporter for real-time monitoring of reversible interactions based on complementation and binding of an exogenous chromophore.

    • Alison G. Tebo
    •  & Arnaud Gautier

  • Article
    | Open Access

    Dynamic combinatorial chemistry (DCC) is instrumental in the discovery of ligands for pharmaceutical targets. Here, the authors adapted DCC to work at 4 degrees Celsius and used it to identify a ligand for Neuronal Calcium Sensor-1 that promotes NCS-1/Ric8a protein-protein interaction.

    • Andrea Canal-Martín
    • , Javier Sastre
    •  & Ruth Pérez-Fernández

  • Article
    | Open Access

    Membrane-anchored DNA probes have been used to study molecular interactions and control cell assembly, but are not selective for different cell membranes. Here the authors develop a lipid-conjugated oligonucleotide for alkaline phosphatase-dependent cell membrane anchorage and use it to distinguish different cancer cells.

    • Cheng Jin
    • , Jiaxuan He
    •  & Weihong Tan

  • Article
    | Open Access

    H3K9me3 and H3K27me3 chromatin silencing marks are usually deposited by different SET-domain proteins. Here the authors show that the Enhancer-of-zeste-like protein Ezl1, from the unicellular eukaryote Paramecium tetraurelia, catalyzes methylation of histone H3 in vitro and in vivo with an apparent specificity toward K9 and K27, and controls the repression of transposable elements.

    • Andrea Frapporti
    • , Caridad Miró Pina
    •  & Sandra Duharcourt

  • Article
    | Open Access

    Single-site labelling of proteins is desirable, e.g., for analytical purposes. Here, the authors developed a method in which they use an aldol-type reaction to modify proteins at N-terminal glycine residues in an efficient and selective manner, which is also applicable to cell lysates.

    • Landa Purushottam
    • , Srinivasa Rao Adusumalli
    •  & Vishal Rai

  • Article
    | Open Access

    Metal ions play essential roles in myriads of biological processes, from catalytic co-factors to supporting protein and nucleic acid structures. Here the authors use long-wavelength X-ray diffraction to locate hundreds of potassium ions taking part in the formation of rRNA tertiary structure, mediating rRNA–protein interactions and supporting ribosomal protein structures and function.

    • Alexey Rozov
    • , Iskander Khusainov
    •  & Gulnara Yusupova

  • Article
    | Open Access

    Acyl carrier proteins (ACPs), a universal and highly conserved carrier of acyl intermediates during fatty acid and polyketide synthesis, are difficult to visualise. Here, the authors developed a facile, Raman spectroscopy-based method to detect ACP-substrate interactions.

    • Samuel C. Epstein
    • , Adam R. Huff
    •  & Louise K. Charkoudian

  • Article
    | Open Access

    Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.

    • Victor A. Streltsov
    • , Sukanya Luang
    •  & Maria Hrmova

  • Article
    | Open Access

    Reversible cysteine modifications play important roles in cellular redox signaling. Here, the authors develop a chemical proteomics strategy that enables the quantitative analysis of endogenous cysteine nitrosylation sites and their dynamic regulation under nitrosative stress conditions.

    • Ruzanna Mnatsakanyan
    • , Stavroula Markoutsa
    •  & René P. Zahedi

  • Article
    | Open Access

    Chemo-enzymatic tandem processes allow access to more complex non-racemic products. Here, the authors show that non-ionic surfactants, especially the tailor-made surfactant TPGS-750-M, enhance the activity of alcohol dehydrogenase to afford stereopure products in a 1-pot reaction.

    • Margery Cortes-Clerget
    • , Nnamdi Akporji
    •  & Bruce H. Lipshutz

  • Article
    | Open Access

    Polyglutamine (polyQ) tracts are low-complexity regions and their expansion is linked to certain neurodegenerative diseases. Here the authors combine experimental and computational approaches to find that the length of the androgen receptor polyQ tract correlates with its helicity and show that the polyQ helical structure is stabilized by hydrogen bonds between the Gln side chains and main chain carbonyl groups.

    • Albert Escobedo
    • , Busra Topal
    •  & Xavier Salvatella

  • Article
    | Open Access

    Bromodomains are conserved protein interaction modules that recognize acetyl-lysine modifications. Here the authors present a set of 25 selective small molecule inhibitors covering 29 human bromodomain targets and comprehensively evaluate the selectivity of this probe-set.

    • Qin Wu
    • , David Heidenreich
    •  & Stefan Knapp

  • Article
    | Open Access

    Ceramides are lipids that act directly on mitochondria to trigger apoptosis, but the underlying mechanism remains largely unclear. Here authors use a photoactivatable ceramide probe combined with a computation approach and functional studies to identify the voltage-dependent anion channel VDAC2 as a direct effector of ceramide-mediated cell death.

    • Shashank Dadsena
    • , Svenja Bockelmann
    •  & Joost C. M. Holthuis

  • Article
    | Open Access

    The understanding of liquid-liquid phase separation is crucial to cell biology and benefits from cell-mimicking in vitro assays. Here, the authors develop a microfluidic platform to study coacervate formation inside liposomes and show the potential of these hybrid systems to create synthetic cells.

    • Siddharth Deshpande
    • , Frank Brandenburg
    •  & Cees Dekker

  • Article
    | Open Access

    The increasing concern of global plastic pollution has led to an increase in the production and characterization of bio-based and biodegradable alternatives. Here the authors show the synthesis of a series of fully bio-based alternatives based on 2,4-, 2,5-, and 2,6- pyridinedicarboxylic acids, via enzymatic catalysis.

    • Alessandro Pellis
    • , James W. Comerford
    •  & Thomas J. Farmer

  • Article
    | Open Access

    Gene expression profiles can classify breast cancer into five clinically relevant subtypes. Here, the authors perform an in-depth quantitative profiling of the proteome of 45 breast tumors, and show they can recapitulate the transcriptome-based classifications and identify many potentially antigenic tumour-specific peptides.

    • Henrik J. Johansson
    • , Fabio Socciarelli
    •  & Janne Lehtiö

  • Article
    | Open Access

    For CRISPR-Cas9 genome editing, Cas9 protein is guided to its target by single guide (sg) RNA. Here, the authors synthesised sgRNAs via convergent ‘click’ ligation of variable 20-mer RNAs that target the genome and a Cas9-binding 79-mer chimeric RNA/2´-OMe RNA of fixed sequence in a single tube.

    • Lapatrada Taemaitree
    • , Arun Shivalingam
    •  & Tom Brown

  • Article
    | Open Access

    Metal-organic frameworks have shown promise as nanoreactors, facilitating the synthesis of molecules that are otherwise difficult to isolate. Here, the authors design a framework featuring unobstructed adenine linkers to which thymine molecules can base-pair, allowing for thymine dimerization in the pores upon UV irradiation.

    • Samantha L. Anderson
    • , Peter G. Boyd
    •  & Kyriakos C. Stylianou

  • Article
    | Open Access

    Clear-cell carcinomas are aggressive tumours characterised by high accumulation of lipids and glycogen. Here, the authors report that these cancers have a common vulnerability to GPX4 inhibition-induced ferroptosis and using CRISPR screen and lipodomic profiling, they identify HIF-2α- HILPDA axis promotes ferroptosis via enrichment of PUFA lipids.

    • Yilong Zou
    • , Michael J. Palte
    •  & Stuart L. Schreiber

  • Article
    | Open Access

    The mechanisms that accommodate variable external dependencies in evolution are not clear. Here, the authors show that switches between external and internal metabolic controls of carotenoid-producing networks in birds are linked to shifts in evolutionary rates, with internalization of control resulting in bursts of evolutionary diversification.

    • Alexander V. Badyaev
    • , Alexander B. Posner
    •  & Dawn M. Higginson

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