Biochemistry articles within Nature

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  • News & Views |

    The Chilean soapbark tree is the source of QS-21 — a valuable but hard-to-obtain vaccine additive. Yeast strains engineered to express all components of the QS-21 biosynthetic pathway provide an alternative route to this therapeutic.

    • Ryan Nett

  • Article
    | Open Access

    An atlas of the substrate specificities for the human tyrosine kinome reveals diversity of motif specificities and enables identification of kinase–substrate relationships and kinase regulation in phosphoproteomics experiments.

    • Tomer M. Yaron-Barir
    • , Brian A. Joughin
    •  & Jared L. Johnson

  • Article |

    A completely genetically encoded boronic-acid-containing designer enzyme was created and characterized using X-ray crystallography, high-resolution mass spectrometry and 11B NMR spectroscopy, allowing chemistry that is unknown in nature and currently not possible with small-molecule catalysts.

    • Lars Longwitz
    • , Reuben B. Leveson-Gower
    •  & Gerard Roelfes

  • Article |

    Two species of auxotrophic marine bacteria are shown to share precursors to synthesize the essential cofactor vitamin B12, and such ligand cross-feeding may be a common phenomenon in the ocean and other ecosystems.

    • Gerrit Wienhausen
    • , Cristina Moraru
    •  & Meinhard Simon

  • Research Briefing |

    A broadly applicable method allows selective, rapid and efficient chemical modification of the side chain of tryptophan amino acids in proteins. This platform enables systematic, proteome-wide identification of tryptophan residues, which can form a bond (called cation–π interaction) with positively charged molecules. Such interactions are key in many biochemical processes, including protein-mediated phase separation.

  • Article |

    We propose a model for a sequential, multistep activation mechanism of metabotropic glutamate receptor subtype 5, including a series of structures in lipid nanodiscs, from inactive to fully active, with agonist-bound intermediate states.

    • Kaavya Krishna Kumar
    • , Haoqing Wang
    •  & Brian K. Kobilka

  • Article
    | Open Access

    Citrate synthase from the cyanobacterium Synechococcus elongatus is shown to self-assemble into Sierpiński triangles, a finding that opens up the possibility that other naturally occurring molecular-scale fractals exist.

    • Franziska L. Sendker
    • , Yat Kei Lo
    •  & Georg K. A. Hochberg

  • Article |

    Glucocorticoids reprogram the mitochondrial metabolism of macrophages, resulting in increased and sustained production of the anti-inflammatory metabolite itaconate and, as a consequence, inhibition of the inflammatory response.

    • Jean-Philippe Auger
    • , Max Zimmermann
    •  & Gerhard Krönke

  • Article
    | Open Access

    Cryo-electron microscopy structures of the human Integrator complex in three different functional states shed light on how Integrator terminates RNA polymerase II (Pol II) transcription by disengaging Pol II from the DNA template.

    • Isaac Fianu
    • , Moritz Ochmann
    •  & Patrick Cramer

  • Article
    | Open Access

    An ensemble of cryo-electron microscopy structures of the KpsMT ABC transporter in complex with the KpsE co-polymerase and a glycolipid substrate reveal how capsular polysaccharides are recognized and translocated across bacterial cell membranes.

    • Jeremi Kuklewicz
    •  & Jochen Zimmer

  • Article
    | Open Access

    Cryo-electron microscopy structures of human RAD51 in complex with the nucleosome show that RAD51 can adopt two conformations—rings and filaments—and reveal how RAD51 binds to the nucleosome through its N-terminal lobe domain.

    • Takuro Shioi
    • , Suguru Hatazawa
    •  & Hitoshi Kurumizaka

  • Article |

    Monoamines and neurotoxicants share a binding pocket in VMAT1 featuring polar sites for specificity and a wrist-and-fist shape for versatility, and monoamine enrichment in storage vesicles arises from dominant import via favoured lumenal-open transition of VMAT1 and protonation-precluded binding during its cytoplasmic-open transition.

    • Jin Ye
    • , Huaping Chen
    •  & Weikai Li

  • Article |

    Time-resolved cryo-EM is used to capture structural transitions during G-protein activation stimulated by a G-protein-coupled receptor.

    • Makaía M. Papasergi-Scott
    • , Guillermo Pérez-Hernández
    •  & Georgios Skiniotis

  • Article
    | Open Access

    Binding of the substrates NAD+ and ATP to the plant Toll/interleukin-1 receptor (TIR) domain proteins induces phase separation and, thereby, activation of TIR enzymatic and immune signalling activity.

    • Wen Song
    • , Li Liu
    •  & Jijie Chai

  • Review Article |

    This Review describes the various mechanisms of ion-coupled transport across membranes and how the activities of transporter proteins are modulated by the composition of the lipid bilayer.

    • David Drew
    •  & Olga Boudker

  • Technology Feature |

    Imaging and molecular manipulation reveal how biomolecular condensates form and offer clues to the role of phase separation in health and disease.

    • Elie Dolgin

  • Article
    | Open Access

    IL-10 exerts its anti-inflammatory activity in macrophages by increasing the expression of enzymes that promote fatty acid desaturation and downstream regulation of the transcription factor REL.

    • Autumn G. York
    • , Mathias H. Skadow
    •  & Richard A. Flavell

  • Article
    | Open Access

    We find that bile salt hydrolase N-acyltransferase activity can form bacterial bile acid amidates that are positively correlated with the colonization of gut bacteria that assist in the regulation of the bile acid metabolic network.

    • Bipin Rimal
    • , Stephanie L. Collins
    •  & Andrew D. Patterson

  • Article
    | Open Access

    Cryo-electron microscopy structures of intermediates formed during the degradation of the 30S ribosomal unit shed light on how the 3′ to 5′ exonuclease ribonuclease R controls the ribosomal degradation process.

    • Lyudmila Dimitrova-Paternoga
    • , Sergo Kasvandik
    •  & Helge Paternoga

  • Article |

    A computational model generates conformational ensembles of 28,058 intrinsically disordered proteins and regions (IDRs) in the human proteome and sheds light on the relationship between sequence, conformational properties and functions of IDRs.

    • Giulio Tesei
    • , Anna Ida Trolle
    •  & Kresten Lindorff-Larsen

  • Article
    | Open Access

    The E3 ligase SIFI is identified as a dedicated silencing factor of the integrated stress response, a finding that has implications for the development of therapeutics for neurodegenerative diseases caused by mitochondrial protein import stress.

    • Diane L. Haakonsen
    • , Michael Heider
    •  & Michael Rapé

  • Article |

    We study the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins, showing how cohesin initially responds to replication and providing a molecular model for the establishment of sister chromatid cohesion.

    • Yasuto Murayama
    • , Shizuko Endo
    •  & Hiroyuki Araki

  • Article
    | Open Access

    Dissection of the nuclear pore complex provides a model in which the HIV capsid enters the nucleus through karyopherin mimicry, a mechanism likely to be conserved across other viruses.

    • C. F. Dickson
    • , S. Hertel
    •  & D. A. Jacques

  • Article
    | Open Access

    Latrophilin-3 organizes synapses through a convergent dual-pathway mechanism in which Gαs signalling is activated and phase-separated postsynaptic protein scaffolds are recruited.

    • Shuai Wang
    • , Chelsea DeLeon
    •  & Thomas C. Südhof

  • News & Views |

    LINE-1 DNA elements self-duplicate, inserting the copy into new regions of the genome — a key process in chromosome evolution. Structures of the machinery that performs this process in humans are now reported.

    • Gael Cristofari

  • Research Briefing |

    The strength of the biological carbon pump was estimated using direct measurements of nutrients collected over decades. The findings indicate that ocean waters can capture and store larger amounts of carbon dioxide than previously estimated. This might have implications for climate-change models.

  • Article |

    Enzyme-bound ketyl radicals derived from thiamine diphosphate are selectively generated through single-electron oxidation by a photoexcited organic dye and shown to lead to enantioselective radical acylation reactions.

    • Yuanyuan Xu
    • , Hongwei Chen
    •  & Xiaoqiang Huang

  • 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

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