Proteomics articles within Nature

Featured

  • 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 |

    VVD-133214, a clinical-stage, covalent allosteric inhibitor of the helicase WRN, was well tolerated in mice and led to robust tumour regression in multiple microsatellite-instability-high colorectal cancer cell lines and patient-derived xenograft models.

    • Kristen A. Baltgalvis
    • , Kelsey N. Lamb
    •  & Todd M. Kinsella

  • Article |

    Global profiling of hyper-reactive tryptophan sites across whole proteomes using tryptophan chemical ligation by cyclization (Trp-CLiC) reveals a systematic map of tryptophan residues that participate in cation–π interactions, including functional sites that can regulate protein-mediated phase-separation processes.

    • Xiao Xie
    • , Patrick J. Moon
    •  & Christopher J. Chang

  • Article
    | Open Access

    A multidimensional proteomics analysis of the interactions between around 2,000 nuclear proteins and over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states provides insights into how chromatin states are decoded by chromatin readers.

    • Saulius Lukauskas
    • , Andrey Tvardovskiy
    •  & Till Bartke

  • 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

  • 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

  • Article
    | Open Access

    Comparisons of phenotypic and genetic association with protein levels from Icelandic and UK Biobank cohorts show that using multiple analysis platforms and stratifying populations by ancestry improves the detection of associations and allows the refinement of their location within the genome.

    • Grimur Hjorleifsson Eldjarn
    • , Egil Ferkingstad
    •  & Kari Stefansson

  • Article
    | Open Access

    The Pharma Proteomics Project generates the largest open-access plasma proteomics dataset to date, offering insights into trans protein quantitative trait loci across multiple biological domains, and highlighting genetic influences on ligand–receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks.

    • Benjamin B. Sun
    • , Joshua Chiou
    •  & Christopher D. Whelan

  • Article |

    A scalable total synthesis of portimines enables structural reassignment of portimine B and in-depth functional evaluation of portimine A, revealing that portimine A induces translation inhibition selectively in human cancer cells and is efficacious in vivo tumour-clearance models.

    • Junchen Tang
    • , Weichao Li
    •  & Phil S. Baran

  • 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

    Analyses of the proteomes of astrocytes and neurons in a cell-specific and subcompartment-specific manner reveal distinct roles for these cell types that are relevant to obsessive–compulsive disorder and perhaps other brain disorders.

    • Joselyn S. Soto
    • , Yasaman Jami-Alahmadi
    •  & Baljit S. Khakh

  • Research Briefing |

    Genetic scores for predicting levels of several types of biomolecule have been developed and validated in people of diverse ancestries, and used to uncover insights into disease biology. An open resource to disseminate these scores, OmicsPred, will enable researchers to predict various molecular traits from genetic profiles in their own data sets.

  • Research Briefing |

    Mitochondria are intracellular organelles that contain a large set of proteins to help them produce energy, among other functions. A systematic analysis reveals how mitochondrial proteins are organized into complexes and assemblies, facilitating the identification of the molecular mechanisms and pathways that underlie the organelle’s many functions.

  • Article
    | Open Access

    An analysis of MitCOM—a comprehensive resource for the identification, organization and interaction of mitochondrial machineries and pathways in yeast—identifies a constitutive pathway for the removal of preproteins.

    • Uwe Schulte
    • , Fabian den Brave
    •  & Thomas Becker

  • Career Column |

    A need for community drove Jennifer Geddes-McAlister to found a network for mothers in science. Here’s what she learnt.

    • Jennifer Geddes-McAlister

  • Spotlight |

    Working at a research hospital allows Fridtjof Lund-Johansen to test the effectiveness of vaccines in people with compromised immune systems.

    • Helen Santoro

  • Nature Index |

    From nano-filters for tackling water pollution to protein fingerprinting that treats disease, these researchers are making their mark on the field.

    • Gemma Conroy
    •  & Benjamin Plackett

  • Research Briefing |

    The organizational principles of the eukaryotic cell cycle have yet to be pinned down, and two opposing models have been put forward. Genetic and proteomics analyses in a model eukaryote, fission yeast, reveal that the cell cycle is organized through a hybrid of both models, although the contribution of one strongly outweighs the other.

  • Article
    | Open Access

    The core cell cycle is largely driven by increasing total CDK activity together with minor differences in the substrate specificity of the CDKs initiating DNA replication and mitosis.

    • Souradeep Basu
    • , Jessica Greenwood
    •  & Paul Nurse

  • Technology Feature |

    Deducing the full protein complement of individual cells has long played second fiddle to transcriptomics. That’s about to change.

    • Jeffrey M. Perkel

  • News & Views |

    An analysis in ageing nematode worms reveals reductions in the tagging of certain proteins for clearance. This can lead to the accumulation of unnecessary proteins, in turn impairing cellular and tissue function.

    • Bart P. Braeckman

  • Article |

    A proximity-dependent biotinylation technique defines the location of more than 4,000 proteins in a human cell, and almost 36,000 proximal interactions between proteins, including those at the interface of the mitochondria and ER.

    • Christopher D. Go
    • , James D. R. Knight
    •  & Anne-Claude Gingras

  • Article |

    Inhibition of YBX1, a downstream target of the Janus kinase JAK2, sensitizes myeloproliferative neoplasm cells to JAK and could provide a means to eradicate such cells in human haematopoietic cancers.

    • Ashok Kumar Jayavelu
    • , Tina M. Schnöder
    •  & Florian H. Heidel

  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray

  • Article |

    During nutrient stress, ribosomal protein abundance is regulated primarily by translational and non-autophagic degradative mechanisms, but ribosome density per cell is largely maintained by reductions in cell volume and rates of cell division.

    • Heeseon An
    • , Alban Ordureau
    •  & J. Wade Harper

  • Article |

    An advanced proteomics workflow is used to identify 340,000 proteins from 100 taxonomically diverse species, providing a comparative view of proteomes across the evolutionary range.

    • Johannes B. Müller
    • , Philipp E. Geyer
    •  & Matthias Mann

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