Protein–protein interaction networks articles within Nature

Featured

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Letter |

    Affinity tagging, mass spectroscopy and a tailor-made scoring system are used to identify 497 high-confidence interactions between human proteins and human immunodeficiency virus proteins.

    • Stefanie Jäger
    • , Peter Cimermancic
    •  & Nevan J. Krogan

  • Article |

    A meta-analysis of genome-wide association studies in more than 66,000 individuals identifies 68 new genomic loci that reliably associate with platelet count and volume, and reveals new gene functions.

    • Christian Gieger
    • , Aparna Radhakrishnan
    •  & Nicole Soranzo

  • News & Views |

    An innovative marriage of techniques, combining the principles of common protein pull-down assays with single-molecule fluorescence microscopy, opens up new ways of visualizing cellular protein complexes. See Article p.484

    • Philip Tinnefeld

  • Technology Feature |

    Developing techniques are helping researchers to build the protein interaction networks that underlie all cell functions.

    • Laura Bonetta

  • Article |

    The two hereditary breast cancer susceptibility genes, BRCA1 and BRCA2, have roles in responding to DNA damage. When they are mutated or absent, genomic instability, a contributory factor to cancer development, results. Studies of BRCA2 have been hampered by its large size, which makes purification of the full-length protein challenging. These authors report the first in vitro characterization of full-length BRCA2 and delineate the different ways by which BRCA2 facilitates RAD51-mediated homologous recombination.

    • Ryan B. Jensen
    • , Aura Carreira
    •  & Stephen C. Kowalczykowski

  • Article |

    Autophagy is a cellular process by which proteins and organelles are sequestered in autophagosomal vesicles and delivered to the lysosome for degradation. Here the authors present a proteomic analysis of the autophagy interaction network in human cells. Their results reveal a network of signalling modules and extensive connectivity among subnetworks. This global view of the mammalian autophagy pathway will be an important resource for future mechanistic understanding of this pathway.

    • Christian Behrends
    • , Mathew E. Sowa
    •  & J. Wade Harper

  • Letter |

    Nascent secretory or membrane proteins contain an amino-terminal signal peptide that mediates their targeting to the plasma membrane (in prokaryotes) or endoplasmic reticulum (in eukaryotes). This peptide is recognized by the signal recognition particle (SRP). A universally conserved component of the SRP is known as SRP54 (Ffh in bacteria). Here, the crystal structure of Sulfolobus solfataricus SRP54 fused to a signal peptide is presented, revealing how the signal peptide is recognized by SRP54.

    • Claudia Y. Janda
    • , Jade Li
    •  & Kiyoshi Nagai

  • News & Views |

    The production of intestinal cells in a worm embryo is regulated by a network of transcription factors. Studies of these networks in mutant worms provide evidence for stochastic effects in gene expression.

    • Adrian Streit
    •  & Ralf J. Sommer

  • Letter |

    Polycomb proteins have a key role in regulating the expression of genes essential for development, differentiation and maintenance of cell fates. Here, Polycomb repressive complex 2 (PRC2) is shown to form a complex with JARID2, a Jumonji domain protein. JARID2 is required for the binding of Polycomb proteins to target genes in embryonic stem cells as well as for the proper differentiation of ES cells.

    • Diego Pasini
    • , Paul A. C. Cloos
    •  & Kristian Helin

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