Proteins articles within Nature Communications

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  • Article |

    The elongation factors DSIF and NELF have established roles in polymerase pausing, elongation and 3'-end processing of replication-dependent histone mRNAs. Here the authors demonstrate that DSIF and NELF form a complex with Integrator and allow proper 3'-processing of snRNA transcripts by preventing the recruitment of CstF.

    • Junichi Yamamoto
    • , Yuri Hagiwara
    •  & Yuki Yamaguchi

  • Article
    | Open Access

    Few tools are available to identify active membrane proteins within their native lipid environment. Here, Gold et al. report on a strategy that can be used for site-specific labelling of membrane proteins via electron cryotomography.

    • Vicki A.M. Gold
    • , Raffaele Ieva
    •  & Werner Kühlbrandt

  • Article |

    The expression of stress-induced ligands and their recognition by the NKG2D-activating receptor is important for the elimination of virally infected and cancerous cells by cytotoxic lymphocytes. Here, the authors provide insights into the post-transcriptional mechanism regulating the expression of the NKG2D ligand, MICB.

    • Daphna Nachmani
    • , Tony Gutschner
    •  & Ofer Mandelboim

  • Article |

    Functional changes in protein structures are involved in a large number of biochemical processes. Here, the authors perform a simulation study of known protein structures to show how β-sheets possess the ability to facilitate concerted backbone motions.

    • R. Bryn Fenwick
    • , Laura Orellana
    •  & Xavier Salvatella

  • Article |

    Membrane protein topogenesis is not fully understood, although the path that proteins take through the ribosome and Sec-complex has been described. Here, Bischoff et al.present the structure of a ribosome-SecY complex containing an intermediate of proteorhodopsin, which provides further insight into this topogenesis.

    • Lukas Bischoff
    • , Stephan Wickles
    •  & Roland Beckmann

  • Article |

    Mice overexpressing the mitochondrial protein MitoNEET in white adipose tissue (WAT) are very fat but metabolically healthy. Here the authors study the physiological consequences of MitoNEET overexpression in WAT, showing that this triggers an initial browning and that the subsequently expanded WAT is less fibrotic.

    • Christine M. Kusminski
    • , Jiyoung Park
    •  & Philipp E. Scherer

  • Article
    | Open Access

    In response to neuronal injury or disease, microglia adopt distinct reactive phenotypes via the expression of proteins, such as the purinergic P2X4 receptor. Here, Masuda et al.show that the transcription factor axis, interferon regulatory factor-8 and -5, drives the expression of P2X4 receptor in microglia and the adoption of a reactive phenotype after peripheral nerve injury.

    • Takahiro Masuda
    • , Shosuke Iwamoto
    •  & Kazuhide Inoue

  • Article |

    The transcriptional effects of auxin signalling are mediated by auxin response factors (ARFs) that interact with inhibitory IAA proteins. Nanao et al.present the crystal structure of domain III/IV of ARF5, revealing the structural basis for its interaction with IAAs and its potential to trigger ARF5 oligomerization.

    • Max H. Nanao
    • , Thomas Vinos-Poyo
    •  & Renaud Dumas

  • Article |

    Glycosylation is an essential process for preservation of protein structure and biological activity. Here, the authors show that the introduction of charge clusters containing specific amino-acid sequences can instead be used to control the stability and activity of non-glycosylated proteins.

    • Nikki Y. Tan
    • , Ulla-Maja Bailey
    •  & Benjamin L. Schulz

  • Article |

    Many biological processes rely on fluctuations in protein structure, but the characterization of extended structural motions is challenging. Here the authors use orientation-sensitive terahertz near-field microscopy to report the optical observation of long-range protein vibrational modes.

    • Gheorghe Acbas
    • , Katherine A. Niessen
    •  & A.G. Markelz

  • Article |

    Asthma is often characterized by Th2-mediated inflammatory responses, which are initiated by lung dendritic cells. Here, Williams et al.demonstrate that dendritic cell expression of transcription factor IRF4 drives Th2 differentiation through IL-33 and IL-10 activation.

    • Jesse W. Williams
    • , Melissa Y. Tjota
    •  & Anne I. Sperling

  • Article |

    Glioblastoma cancers contain brain tumour-initiating cells and targeting these specific cells is an attractive opportunity for therapy. In this study, the authors show that FOXG1 and Groucho/TLE transcription factors are important for glioblastoma growth and might be useful therapeutic targets.

    • Federica Verginelli
    • , Alessandro Perin
    •  & Stefano Stifani

  • Article |

    The Wnt receptor Frizzled binds its endogenous ligand via a cysteine-rich domain; however, the function of the equivalent domain in Smoothened, a mediator of Hedgehog signalling, is unknown. Rana et al.present the NMR solution structure of this domain, and characterize its interaction with the glucocorticoid budesonide.

    • Rajashree Rana
    • , Candace E. Carroll
    •  & Jie J. Zheng

  • Article |

    ϕ analysis provides a means to tease apart the dynamics of fast conformational changes in proteins by analysing the thermodynamic impact of point mutations. Purohit et al.apply this approach on a grand scale to map energy changes associated with the opening and closing of an acetylcholine receptor.

    • Prasad Purohit
    • , Shaweta Gupta
    •  & Anthony Auerbach

  • Article
    | Open Access

    The cyanobacterial circadian oscillator comprises an autoregulatory loop that is driven by phosphorylation and dephosphorylation of the hexameric kinase KaiC. Kitayama et al.reveal how interactions between KaiC subunits regulate its catalytic activities and ensure robust circadian behaviour.

    • Yohko Kitayama
    • , Taeko Nishiwaki-Ohkawa
    •  & Takao Kondo

  • Article |

    The Caenorhabditis elegans neuropeptide NLP-22 is regulated by a larval circadian clock that is similar to circadian clocks in mammals. Nelson et al. show that NLP-22, expressed in Caenorhabditis elegansRIA interneurons, regulates a sleep-like behavioural quiescence.

    • M.D. Nelson
    • , N.F. Trojanowski
    •  & D.M. Raizen

  • Article |

    Whether microRNA processing mediated by Dicer is regulated in a cell-cycle-dependent manner is unknown. Here, Chen et al.show that Cyclin D1, which is important in the control of the cell cycle, regulates the expression of Dicer, and that Cyclin D1 and Dicer expression levels correlate in breast cancer.

    • Zuoren Yu
    • , Liping Wang
    •  & Richard G. Pestell

  • Article
    | Open Access

    Screens for protein–protein interactions and for drugs that disrupt them typically use in vitro assays which fail to capture the complexity of the cell’s interior. By fixing proteins to distinct cellular locations, Herce et al.demonstrate a fluorescent-three-hybrid approach to probe such interactions in their cellular contexts.

    • Henry D. Herce
    • , Wen Deng
    •  & M. Cristina Cardoso

  • Article
    | Open Access

    Components of the complement system have been shown to promote liver regeneration. Haynes et al. demonstrate that the complement fragment C3a can induce regeneration of the embryonic chick retina from stem and progenitor cells of the ciliary margin via activation of STAT3 and other downstream signalling pathways.

    • Tracy Haynes
    • , Agustin Luz-Madrigal
    •  & Katia Del Rio-Tsonis

  • Article
    | Open Access

    Bacterial endonuclease V enzymes are characterized as DNA repair proteins. Here the authors show that human endonuclease V is an inosine-specific ribonuclease, indicating a role for this enzyme in normal RNA metabolism rather than DNA repair.

    • Erik Sebastian Vik
    • , Meh Sameen Nawaz
    •  & Ingrun Alseth

  • Article
    | Open Access

    In Escherichia coli, the highly conserved enzyme endonuclease V has a role in DNA repair. Here the authors show that human endonuclease V is an inosine 3' endoribonuclease and that Tudor Staphylococcal nuclease enhances this activity, suggesting a role for human endonuclease V in RNA metabolism.

    • Yoko Morita
    • , Toshihiro Shibutani
    •  & Isao Kuraoka

  • Article |

    The expression of specific genes can be controlled by the combination of DNA-binding proteins, which determines their binding site selectivity. Here, simplified synthetic basic region leucine zipper-based peptides are induced to dimerize either through their C- or N-terminus, and thus are targeted to different DNA sequences.

    • Jesús Mosquera
    • , Adrián Jiménez-Balsa
    •  & José L Mascareñas

  • Article |

    Dynamin promotes membrane fission by constricting the neck of invaginating membranes; however, it was recently shown that dynamin also regulates membrane fusion. Here the authors show that this fusogenic activity is mediated by interaction with the Qa SNARE, thereby promoting trans-SNARE formation.

    • Kannan Alpadi
    • , Aditya Kulkarni
    •  & Christopher Peters

  • Article |

    An important challenge in the bottom-up fabrication of artificial tissues is communication between compartments bounded by lipid bilayers. Mantri et al. engineer a dimeric transmembrane pore that, like eukaryotic gap junctions, can form a conductive pathway between adjacent bilayers.

    • Shiksha Mantri
    • , K. Tanuj Sapra
    •  & Hagan Bayley

  • Article |

    RecA/Rad51 proteins catalyse the recognition and exchange between two homologous DNA strands during homologous recombination. Sasanuma et al. now demonstrate that Rad51 association with ssDNA is mediated by a complex consisting of Psy3, Csm2, Shu1 and Shu2 proteins.

    • Hiroyuki Sasanuma
    • , Maki S. Tawaramoto
    •  & Akira Shinohara

  • Article
    | Open Access

    The transcriptional repressor NKAP is required at an early stage of T cell development for the differentiation of αβ T cells. Thapa et al.now show that at a later stage, NKAP has a specific role in positive selection of double positive thymocytes into the iNKT cell lineage.

    • Puspa Thapa
    • , Joy Das
    •  & Virginia Smith Shapiro

  • Article |

    COG complexes are thought to be involved in tethering of intra-Golgi vesicles. Here the authors show that individual COG complex subunits direct the assembly of distinct vesicle-tethering platforms, suggesting that COG subunits have a role in the specificity of vesicular sorting.

    • Rose Willett
    • , Tetyana Kudlyk
    •  & Vladimir Lupashin

  • Article |

    The ‘on’ and ‘off’ states of the photoswitchable protein Dronpa have been characterized, but the interconversion process remains poorly understood. Here the authors perform time-resolved ultrafast infrared measurements to follow both the structural changes and proton transfer events that occur during conversion.

    • Mark M. Warren
    • , Marius Kaucikas
    •  & Jasper J. van Thor

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