Proteins articles within Nature Communications

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  • 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

  • Article |

    Trichoplaxis the most primitive multicellular animal on Earth and thus provides insight into the earliest stages of evolution. Delving deep into the proteome, Heck and colleagues observe a burst in tyrosine phosphorylation, confirming the hypothesis that at the onset of this new communication system a surplus of phosphorylation took place.

    • Jeffrey H. Ringrose
    • , Henk W.P. van den Toorn
    •  & Albert J.R. Heck

  • Article
    | Open Access

    Levels of extracellular calcium can increase at sites of infection and inflammation; however, the physiological significance of this has been unclear. This work shows that extracellular calcium acts as a danger signal, triggering the NLRP3 inflammasome via two G protein-coupled receptors.

    • Manuela Rossol
    • , Matthias Pierer
    •  & Ulf Wagner

  • Article
    | Open Access

    How the genome is physically organized is less understood in archaea than in eubacteria or eukaryotes. Laurens et al. measure DNA binding by the Sulfolobus solfataricusproteins Alba1 and Alba2 using single-molecule techniques and conclude that the presence of Alba2 leads to more bridging between DNA.

    • Niels Laurens
    • , Rosalie P.C. Driessen
    •  & Gijs J.L. Wuite

  • Article
    | Open Access

    Host–pathogen relationships can be mediated by polyvalent glycan ligand–protein interactions. Here well-defined highly valent glycodendrimeric constructs are synthesized that can mimic pathogens, and can inhibit a model of infection by the Ebola virus.

    • Renato Ribeiro-Viana
    • , Macarena Sánchez-Navarro
    •  & Benjamin G. Davis

  • Article
    | Open Access

    Proteins are integrated into cellular membranes either co-translationally through Sec/SRP or post-translationally by chaperones. These authors show that an integration-dedicated chaperone inE. coli, MPIase, is a glycolipid and facilitates protein insertion into the inner membrane of the bacterium.

    • Ken-ichi Nishiyama
    • , Masahide Maeda
    •  & Keiko Shimamoto

  • Article |

    Multifunctional S100 proteins are upregulated in brain injury, but their role in neurodegeneration is not clear. Dmytriyeva and colleagues study in vivomodels of brain trauma and find that the S100A4 protein and its peptide mimetics protect neurons via the interleukin-10 receptor and the Janus kinase (JAK)/STAT pathway.

    • Oksana Dmytriyeva
    • , Stanislava Pankratova
    •  & Darya Kiryushko

  • Article |

    Rapid synaptic transmission requires efficient recycling of synaptic vesicle membrane proteins. Sochackiet al.use live cell, electron and super-resolution microscopy to visualize exocytosis of vesicular transporters and their rapid recapture in clathrin-rich microdomains in the plasma membrane.

    • Kem A. Sochacki
    • , Ben T. Larson
    •  & Justin W. Taraska

  • Article
    | Open Access

    Cyclin B–Cdk1 is thought to be synonymous with the promoting factor that drives entry into M-phase of the cell cycle. Here, Greatwall kinase is shown to be required for the breakdown of the nuclear envelope and the assembly of the spindle on entry into M-phase, suggesting that it too is a part of the M-phase-promoting factor.

    • Masatoshi Hara
    • , Yusuke Abe
    •  & Takeo Kishimoto

  • Article
    | Open Access

    Many drugs exist that target the β-adrenergic receptor, but they have different efficacies. Kofukuet al. use NMR to show that methionine 82 in the transmembrane domain undergoes conformational changes depending on whether agonists or inverse agonists are bound, explaining the differential drug efficacy.

    • Yutaka Kofuku
    • , Takumi Ueda
    •  & Ichio Shimada

  • Article |

    The mitochondrial transcription factor A (TFAM) mediates both mitochondrial transcription and DNA compaction, but how it achieves these two functions is unknown. In this study, TFAM is shown to slide along DNA and cause local melting, suggesting a mechanism for how TFAM modulates both transcription and compaction.

    • Géraldine Farge
    • , Niels Laurens
    •  & Gijs J.L. Wuite

  • Article
    | Open Access

    Following retinalcis/trans isomerisation, the active form of the G-protein-coupled receptor rhodopsin decays to opsin and all-trans-retinal. In this study, arrestin, a regulator of G-protein-coupled receptor activity, is shown to facilitate the concurrent sequestering of toxic all-trans-retinal and regeneration of 11-cis-retinal within the opsin population.

    • Martha E. Sommer
    • , Klaus Peter Hofmann
    •  & Martin Heck

  • Article
    | Open Access

    Fbw7 is a ubiquitin-ligase, which targets several oncoproteins for proteolysis, and is therefore important for the control and prevention of tumorigenesis. In this study, Arabi and colleagues carry out a proteomic screen of the targets of Fbw7, and identify Nuclear Factor of κ-B2 as a substrate.

    • Azadeh Arabi
    • , Karim Ullah
    •  & Olle Sangfelt

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