Biochemistry articles within Nature

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  • Article
    | Open Access

    Human LINE-1 ORF2p relies on upstream single-stranded target DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break.

    • Akanksha Thawani
    • , Alfredo Jose Florez Ariza
    •  & Kathleen Collins

  • Article |

    Structures of human vesicular monoamine transporter 2 in complexes with serotonin and three clinical drugs provide insights into the structural basis for serotonin transport and inhibition of transporter activity by the drugs.

    • Di Wu
    • , Qihao Chen
    •  & Daohua Jiang

  • Article
    | Open Access

    A new discovery strategy, ‘reverse metabolomics’, facilitates high-throughput matching of mass spectrometry spectra in public untargeted metabolomics datasets, and a proof-of-concept experiment identified an association between microbial bile amidates and inflammatory bowel disease.

    • Emily C. Gentry
    • , Stephanie L. Collins
    •  & Pieter C. Dorrestein

  • Research Briefing |

    A series of structures of the eukaryotic protein-synthesis machinery are imaged at high resolution in defined states of the elongation phase of protein synthesis. Analysis suggests that there are underlying molecular mechanisms that increase the accuracy of translation of genetic information in eukaryotes.

  • Article |

    The accuracy of eukaryotic ribosome translocation relies on eukaryote-specific elements of the 80S ribosome, elongation factor 2 and transfer RNAs, all of which contribute to the maintenance of the messenger RNA reading frame.

    • Nemanja Milicevic
    • , Lasse Jenner
    •  & Gulnara Yusupova

  • Article
    | Open Access

    Analysis of the group II intron ribonucleoprotein shows the molecular interactions involved in branchpoint adenosine recognition, lariat formation and exon ligation, providing clues to the evolutionary conservation of structural components and catalytic mechanisms in premessenger RNA splicing.

    • Ling Xu
    • , Tianshuo Liu
    •  & Anna Marie Pyle

  • Technology Feature |

    As a tech-hungry world gobbles up rare-earth elements, researchers are adapting bacteria that can isolate and purify the metals in the absence of harsh chemicals.

    • Amber Dance

  • Article
    | Open Access

    A protein interaction network constructed with data from high-throughput affinity enrichment coupled to mass spectrometry provides a highly saturated yeast interactome with 31,004 interactions, including low-abundance complexes, membrane protein complexes and non-taggable protein complexes.

    • André C. Michaelis
    • , Andreas-David Brunner
    •  & Matthias Mann

  • Article
    | Open Access

    An analysis of the evolutionary distribution of predicted structures for the metamorphic protein KaiB using AF-Cluster reveals that both conformations of KaiB were distributed in clusters across the KaiB family.

    • Hannah K. Wayment-Steele
    • , Adedolapo Ojoawo
    •  & Dorothee Kern

  • Article
    | Open Access

    A cryo-electron tomography study reports the structure of thick myosin filaments of mouse cardiac muscle in the relaxed state in situ and the MyBP-C links that connect them with the surrounding thin actin filaments.

    • Davide Tamborrini
    • , Zhexin Wang
    •  & Stefan Raunser

  • Article
    | Open Access

    Upon hyperpolarization, the S4 voltage-sensing segment of sea urchin SLC9C1 moves down, removing inhibition caused by an intracellular helix and enabling Na+/H+ exchange, leading to pH-dependent activation of sAC and sperm chemotaxis.

    • Hyunku Yeo
    • , Ved Mehta
    •  & David Drew

  • Book Review |

    An exploration of nature’s toxins reveals complex relationships between humans and the plant chemicals we use as foods, medicines and mind-altering drugs.

    • Emily Monosson

  • News & Views |

    Proteins can condense to form membraneless organelles, which act as vessels for biochemical reactions in cells. An investigation shows that protein condensation is also a cellular mechanism for controlling water availability.

    • J. Pedro de Souza
    •  & Howard A. Stone

  • Article
    | Open Access

    The Bacteroides fragilis type III CRISPR protein Cmr conjugates ATP to S-adenosyl methionine, generating S-adenosyl methionine (SAM)-AMP, a novel second messenger with a role in antiviral signalling.

    • Haotian Chi
    • , Ville Hoikkala
    •  & Malcolm F. White

  • Article
    | Open Access

    Water thermodynamics drive changes in macromolecular assembly that rapidly restore intracellular water availability in response to physiological fluctuations in temperature, pressure and osmotic strength.

    • Joseph L. Watson
    • , Estere Seinkmane
    •  & Emmanuel Derivery

  • Technology Feature |

    Linking mass spectrometry with cryo-electron microscopy could transform understanding of complex protein structures — if scientists can show that samples remain intact when they hit their target.

    • Michael Eisenstein

  • News & Views |

    Evolution by natural selection peerlessly describes how life’s complexity develops — but can it be explained in terms of physics? A new approach suggests it can.

    • George F. R. Ellis

  • Article
    | Open Access

    The endoribonuclease PUCH, a trimer of Schlafen-like-domain proteins, initiates piRNA processing in the nematode Caenorhabditis elegans through 5′-end piRNA precursor cleavage.

    • Nadezda Podvalnaya
    • , Alfred W. Bronkhorst
    •  & René F. Ketting

  • Article
    | Open Access

    The extent to which the AlphaFold database has structurally illuminated proteins that are challenging to annotate for function or putative biological role using standard homology-based approaches at high predicted accuracy is investigated.

    • Janani Durairaj
    • , Andrew M. Waterhouse
    •  & Joana Pereira

  • Article
    | Open Access

    Triacylglycerols are an energy source produced in humans by DGAT1 and DGAT2, but disrupting these enzymes reveals a noncanonical pathway involving the protein DIESL (formerly TMEM68) and its regulator TMX1, which is important during lipid scarcity.

    • Gian-Luca McLelland
    • , Marta Lopez-Osias
    •  & Thijn R. Brummelkamp

  • Article |

    A study describes the metabolic adaptations supporting differentiation, survival and function of tissue-resident memory CD8+ T cells and how to leverage them to enhance immunity against pathogens and tumours.

    • Miguel Reina-Campos
    • , Maximilian Heeg
    •  & Ananda W. Goldrath

  • Article
    | Open Access

    Several independent lines of evidence demonstrated long-term potentiation induction by a structural function of calmodulin-dependent protein kinase II rather than by its enzymatic activity.

    • Jonathan E. Tullis
    • , Matthew E. Larsen
    •  & K. Ulrich Bayer

  • Article
    | Open Access

    Bacteriophage T4 uses an enzyme known as ADP-ribosyltransferase ModB to modify the translational apparatus of bacteria it infects, not only by ADP-ribosylating proteins, but also by attaching entire RNA chains in a process known as RNAylation.

    • Maik Wolfram-Schauerte
    • , Nadiia Pozhydaieva
    •  & Katharina Höfer

  • Article
    | Open Access

    This study highlights the role of mitochondrial complex I-dependent NAD+ regeneration in directing lung epithelial cell fate during postnatal alveolar development by preventing pathological integrated stress response induction.

    • SeungHye Han
    • , Minho Lee
    •  & Navdeep S. Chandel

  • Article
    | Open Access

    Structures of the glucagon receptor bound to β-arrestin 1 are reported, providing further information about the arrestin-mediated modulation of G protein-coupled receptors.

    • Kun Chen
    • , Chenhui Zhang
    •  & Beili Wu

  • News & Views |

    A revised conceptual model of the chemical and physical forms of iron in the ocean reconciles the mismatch between observations and simulations of the amount of dissolved iron in seawater — and might aid climate predictions.

    • Brandy M. Toner

  • Article
    | Open Access

    Tim17 contains conserved negative charges close to the intermembrane space side of the bilayer, which are essential to initiate presequence protein translocation along a distinct transmembrane cavity of Tim17 for both classes of preproteins.

    • Laura F. Fielden
    • , Jakob D. Busch
    •  & Nils Wiedemann

  • Article |

    Cryo-electron microscopy structures and biochemical analyses provide insight into how short prokaryotic Argonaute proteins are assembled and activated, and reveal that oligomerization has a key role in driving catalytic activity.

    • Zhangfei Shen
    • , Xiao-Yuan Yang
    •  & Tian-Min Fu

  • News & Views |

    The 1963 discovery that even the vast oceans were highly contaminated with lead from car exhausts sparked debate and policy changes that benefited the health of millions — and revolutionized the practices of marine biogeochemistry.

    • Jerome Nriagu

  • Research Briefing |

    Protein sequences vary widely in their folding stabilities (the energetic favourability of folded compared with unfolded conformations), and protein alterations that affect stability have profound effects on evolution, health and disease, and biotechnological applications. An innovative method has made it possible to measure these stabilities on a massive scale, revealing evolutionary trends and opening up possibilities for machine learning.

  • Article
    | Open Access

    Fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks yields a generative model for protein design that achieves outstanding performance on a wide range of protein structure and function design challenges.

    • Joseph L. Watson
    • , David Juergens
    •  & David Baker

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