Proteomics articles within Nature

Featured

  • 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

  • Article |

    SARS-CoV-2 modulates central cellular pathways, such as translation, splicing, carbon metabolism, proteostasis and nucleic acid metabolism, in human cells; these pathways can be inhibited by small-molecule inhibitors to prevent viral replication in the cells.

    • Denisa Bojkova
    • , Kevin Klann
    •  & Christian Münch

  • Article |

    A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

    • David E. Gordon
    • , Gwendolyn M. Jang
    •  & Nevan J. Krogan

  • Technology Feature |

    Researchers are finally uncovering the truth about glycans — the sugar-based chains that coat cells and decorate many proteins.

    • Jyoti Madhusoodanan

  • Article |

    The lactylation of lysine residues on histones in mammalian cells is stimulated by hypoxia and bacterial challenges, and increased histone lactylation induces genes involved in wound healing.

    • Di Zhang
    • , Zhanyun Tang
    •  & Yingming Zhao

  • Technology Feature |

    In the age of immunotherapy, cancer biologists are relying on a new generation of tools to learn how the interplay between tumours and immune cells shapes the course of disease.

    • Michael Eisenstein

  • Letter |

    Integrative analyses identify host proteins that are modulated by Zika virus at multiple levels and provide a comprehensive framework for the understanding of Zika virus-induced changes to cellular pathways.

    • Pietro Scaturro
    • , Alexey Stukalov
    •  & Andreas Pichlmair

  • Letter |

    A subset of synaptic proteins are cumulatively phosphorylated during wakefulness and dephosphorylated during sleep, in accordance with sleep need; this may represent a common mechanism underlying regulation of both synaptic homeostasis and sleep–wake homeostasis.

    • Zhiqiang Wang
    • , Jing Ma
    •  & Qinghua Liu

  • Technology Feature |

    Improvements in mapping protein–protein interactions are allowing researchers to deconstruct the delicate mechanics of cells.

    • Marissa Fessenden

  • Letter |

    SCAF1 is always required for the interaction between the respiratory chain complexes III and IV, and in animals carrying only the short isoform of SCAF1, the respirasome is absent in most tissues, with the exception of heart and skeletal muscle, where COX7A2 is present instead of SCAF1.

    • Sara Cogliati
    • , Enrique Calvo
    •  & José Antonio Enriquez

  • Article |

    The effect of natural genetic diversity on the proteome is characterized using an outbred mouse model with extensive variation; both transcripts and proteins from mouse livers are quantified to identify a large set of protein quantitative trait loci (pQTL), and mediation analysis identifies causal protein intermediates of distant pQTL.

    • Joel M. Chick
    • , Steven C. Munger
    •  & Steven P. Gygi

  • Letter |

    Small molecules are powerful tools for investigating protein function, and can serve as leads for new therapeutics, but most human proteins lack known small-molecule ligands; here, a quantitative analysis of cysteine-reactive small-molecule fragments screened against thousands of proteins is reported.

    • Keriann M. Backus
    • , Bruno E. Correia
    •  & Benjamin F. Cravatt

  • Article |

    A new deep proteomic analysis method is used to identify proteins that interact with wild-type cystic fibrosis transmembrane conductance regulator (CFTR) and its mutant version that is the major cause of cystic fibrosis.

    • Sandra Pankow
    • , Casimir Bamberger
    •  & John R. Yates III

  • Outlook |

    The effort to catalogue proteins goes deeper in a push to make genetics research deliver practical benefits.

    • Neil Savage

  • Article |

    Using biochemical fractionation and mass spectrometry, animal protein complexes are identified from nine species in parallel, and, along with genome sequence information, complex conservation is investigated and over one million protein–protein interactions are predicted in 122 eukaryotes.

    • Cuihong Wan
    • , Blake Borgeson
    •  & Andrew Emili

  • Technology Feature |

    The processes behind neuronal communication have not yet been resolved in detail, but dyes, microscopy and protein analysis are beginning to fill in the gaps.

    • Vivien Marx

  • Technology Feature |

    The first draft of the complete human proteome has been more than a decade in the making. In the process, the effort has also delivered lessons about technology and biology.

    • Vivien Marx

  • Article |

    A mass-spectrometry-based draft of the human proteome and a public database for analysis of proteome data are presented; assembled information is used to estimate the size of the protein-coding genome, to identify organ-specific proteins, proteins predicting drug resistance or sensitivity, and many translated long intergenic non-coding RNAs, and to reveal conserved control of protein abundance.

    • Mathias Wilhelm
    • , Judith Schlegl
    •  & Bernhard Kuster

  • Article |

    A draft map of the human proteome is presented here, accounting for over 80% of the annotated protein-coding genes in humans; some novel protein-coding regions, including translated pseudogenes, non-coding RNAs and upstream open reading frames, are identified.

    • Min-Sik Kim
    • , Sneha M. Pinto
    •  & Akhilesh Pandey

  • Letter |

    A large-scale analysis of variation in human protein levels between individuals is performed using mass-spectrometry-based proteomic technology, and a number of protein quantitative trait loci are identified; over 5% of proteins vary by more than 1.5-fold in their expression levels between individuals, and this variation is not always linked to RNA level.

    • Linfeng Wu
    • , Sophie I. Candille
    •  & Michael Snyder

  • Letter |

    High-throughput peptide synthesis and mass spectrometry are used to generate a near-complete reference map of the Saccharomyces cerevisiae proteome; two versions of the map (supporting discovery- and hypothesis-driven proteomics) are then applied to a protein-based quantitative trait locus analysis.

    • Paola Picotti
    • , Mathieu Clément-Ziza
    •  & Ruedi Aebersold

  • Article
    | Open Access

    A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

    • Mark B. Gerstein
    • , Anshul Kundaje
    •  & Michael Snyder

  • Letter |

    A survey of 1,590 putative integral, peripheral and lipid-anchored membrane proteins from Saccharomyces cerevisiae reveals unexpected physical associations underlying the membrane biology of eukaryotes and delineates the global topological landscape of the membrane interactome.

    • Mohan Babu
    • , James Vlasblom
    •  & Jack F. Greenblatt

  • Review Article |

    Over the past ten years, protein engineering has established biocatalysis as a practical and environmentally friendly alternative to traditional forms of catalysis both in the laboratory and in industry.

    • U. T. Bornscheuer
    • , G. W. Huisman
    •  & K. Robins

  • Technology Feature |

    As increasing numbers of protein–protein interactions are identified, researchers are finding ways to interrogate these data and understand the interactions in a relevant context.

    • Monya Baker

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