Proteins articles within Nature Communications

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  • Article
    | Open Access

    Human mitochondrial aspartate/glutamate carriers, citrin and aralar, are regulated by calcium. Here, the authors report the dimeric structure of calcium-free and -bound versions of the regulatory domains to elucidate calcium-dependent conformational changes that could regulate access of substrate to the carrier domain.

    • Chancievan Thangaratnarajah
    • , Jonathan J. Ruprecht
    •  & Edmund R. S. Kunji

  • Article
    | Open Access

    Polycystins (PC) 1 and 2 are large transmembrane proteins that play a vital role in the function of primary cilia. Here, Kim et al. identify the requirements for polycystin trafficking to the cilium, involving a PC1–PC2 interaction, PC1 proteolytic cleavage and a specific trafficking module at the trans-Golgi network.

    • Hyunho Kim
    • , Hangxue Xu
    •  & Feng Qian

  • Article
    | Open Access

    CpG islands are high GC content DNA elements that surround the majority of transcriptional start sites in eukaryotes. Here, the authors analyse over 200 genomic data sets to provide new insight into global CpG islands-dependent regulatory mechanisms in differentiated and pluripotent stem cells.

    • Samuel Beck
    • , Bum-Kyu Lee
    •  & Jonghwan Kim

  • Article |

    Cellular senescence involves extensive structural changes to chromatin, but the role of histone variants and histone cleavage is unknown. Here, Duarte et al.identify histone variant H3.3 and its proteolytically processed form lacking a portion of the N-terminal tail as key regulators of senescence.

    • Luis F. Duarte
    • , Andrew R. J. Young
    •  & Emily Bernstein

  • Article |

    The translocation and assembly module (TAM) is a nanomachine responsible for assembly of proteins into the outer membrane of pathogenic bacteria. Here, Shen et al.use magnetic contrast neutron reflectrometry to visualize movements within the TAM and insertion of a substrate protein into the lipid bilayer.

    • Hsin-Hui Shen
    • , Denisse L. Leyton
    •  & Trevor Lithgow

  • Article |

    Understanding the molecular basis of receptor activation requires characterizing the dynamic equilibrium of conformational states. Here the authors show that the metabotropic glutamate receptor oscillates between conformations on a sub-millisecond timescale, and agonists quantitatively shift the equilibrium towards the activated state based on their potency.

    • Linnea Olofsson
    • , Suren Felekyan
    •  & Emmanuel Margeat

  • Article
    | Open Access

    Integral membrane proteins laterally partition from the SecYEG translocon into the phospholipid bilayer. Here, the authors use photo-induced electron transfer to show that ribosome binding induces the opening of the lateral gate, and demonstrate that lateral opening does not happen at low temperature.

    • Yan Ge
    • , Albena Draycheva
    •  & Wolfgang Wintermeyer

  • Article |

    Opsin has recently been shown to equilibrate phospholipids across the photoreceptor disc membranes. Goren et al.demonstrate that the large conformational changes driven by exposure to light are not required for this activity, and provide insight into the potential mechanisms of lipid translocation.

    • Michael A. Goren
    • , Takefumi Morizumi
    •  & Anant K. Menon

  • Article
    | Open Access

    chTOG, a microtubule polymerase, interacts with TACC3 during mitosis to regulate spindle formation. By studying their Xenopus homologues, Mortuza et al. discover that one TACC3 recruits two chTOG molecules to the spindle, increasing its local concentration and promoting microtubule elongation.

    • Gulnahar B. Mortuza
    • , Tommaso Cavazza
    •  & Guillermo Montoya

  • Article |

    Myelination of peripheral axons by Schwann cells is essential for proper transmission of nerve signals but the underlying mechanisms are not completely understood. Here the authors show that metabolic changes are required to ensure Schwann cell differentiation and proper myelination, and involve the tumour suppressor Lkb1 in regulating this process.

    • Shabnam Pooya
    • , Xiaona Liu
    •  & Biplab Dasgupta

  • Article |

    Complexin binds to synaptic vesicles and inhibits spontaneous exocytosis. Here Snead et al. show that the high curvature of the vesicle membrane is important for membrane binding, and induces a conformational change that is important for complexin’s inhibitory function.

    • David Snead
    • , Rachel T. Wragg
    •  & David Eliezer

  • Article |

    Alpha-2-macroglobulins are protease inhibitors that function as part of eukaryotic innate immunity. Here, Wong and Dessen solve structures of Salmonella alpha-2-macroglobulin and show that it probably serves as part of a rudimentary bacterial immune system in a similar way to the eukaryotic counterpart.

    • Steve G. Wong
    •  & Andréa Dessen

  • Article |

    Membrane curvature and lipid composition direct the binding of many peripheral membrane proteins. Here, Vanni et al. use a combination of in vitroand molecular dynamics approaches to quantify how lipid-packing defects in membranes of various composition and curvature dictate the membrane adsorption of a model lipid-binding protein.

    • Stefano Vanni
    • , Hisaaki Hirose
    •  & Romain Gautier

  • Article |

    The crystal structure of the A2A GPCR suggested that water molecules might form a continuous pathway that becomes disrupted during receptor activation. Here Yuan et al.instead show that a conserved layer of hydrophobic residues forms a gate that opens to form a continuous water channel upon receptor activation.

    • Shuguang Yuan
    • , Slawomir Filipek
    •  & Horst Vogel

  • Article
    | Open Access

    The transcription factor E2F is critical for determining cell proliferation. By monitoring E2F activity in single cells throughout the cell cycle, Dong et al.provide evidence that Myc and G1 cyclin/CDKs regulate different aspects of E2F temporal dynamics, resulting in distinct phenotypic outputs.

    • Peng Dong
    • , Manoj V. Maddali
    •  & Lingchong You

  • Article |

    Following their internalization, G protein-coupled receptors may continue to signal from endosomes through downstream proteins such as Gαs. Rosciglione et al. reveal that Gαsalso regulates the onward trafficking of these receptors from endosomes to lysosomes by interacting with components of the ESCRT complex.

    • Stéphanie Rosciglione
    • , Caroline Thériault
    •  & Christine Lavoie

  • Article
    | Open Access

    G-protein coupled receptors can signal through G-proteins or through β-arrestin, however mechanisms determining pathway selection remain unclear. Here the authors show that the duration of cannabinoid receptor clustering in clathrin coated pits prior to endocytosis determines the strength of β-arrestin signalling.

    • Jacqueline Flores-Otero
    • , Kwang H. Ahn
    •  & Guillermo A. Yudowski

  • Article |

    Mutations resulting in cell transformation occur in single cells to begin with and these cells can be eliminated from epithelial layers. Here, the authors describe a mechanism whereby neighbouring normal cells mediate this extrusion using filamin and intermediate filament, vimentin.

    • Mihoko Kajita
    • , Kaoru Sugimura
    •  & Yasuyuki Fujita

  • Article |

    Some viruses possess ‘decoration’ proteins, such as gpD in lambda phage, that stabilize the viral particles in poorly understood ways. Here the authors show that gpD incorporation into lambda particles provides mechanical reinforcement and increased resistance to punctual deformations and collisions.

    • M. Hernando-Pérez
    • , S. Lambert
    •  & P. J. de Pablo

  • Article
    | Open Access

    Although many proteins adopt uneven distributions in the plasma membrane, it is not clear how these nanoscale heterogeneities relate to the general protein patterning of the membrane. Saka et al. use click chemistry to reveal the mesoscale organization of membrane proteins into multi-protein assemblies.

    • Sinem K. Saka
    • , Alf Honigmann
    •  & Silvio O. Rizzoli

  • Article |

    Despite numerous previous studies, the nature of the interaction of transcription factors (TF) with their endogenous response elements (REs) has remained unclear. Here the authors characterize the binding of p53 and glucocorticoid receptor to their endogenous REs and find that transcriptionally productive interactions are transient and involve only a small fraction of cellular TF molecules.

    • Tatsuya Morisaki
    • , Waltraud G. Müller
    •  & James G. McNally

  • Article |

    PTEN is a prominent tumour suppressor and monitoring its conformation and activity are key to developing targeted therapies. Here, the authors develop a bioluminescence resonance energy transfer biosensor for PTEN conformation and identify novel G protein-coupled receptor regulation and therapeutic activation.

    • Evelyne Lima-Fernandes
    • , Stanislas Misticone
    •  & Mark G.H. Scott

  • Article |

    It was suggested that despite the conservation of their components, yeast and human pol II initiation complexes diverged in architecture. Mühlbacher et al.now demonstrate that the yeast and human core complexes are structurally conserved and provide insight into the conformations adopted by TFIIF during initiation.

    • Wolfgang Mühlbacher
    • , Sarah Sainsbury
    •  & Patrick Cramer

  • Article |

    The study of cell membrane proteins can be simplified by incorporating them into lipid bilayers, but doing this for multiple proteins can be challenging. Here, the authors present a technique to achieve this, and show reconstitution of a bacterial respiratory chain from individual components.

    • Gustav Nordlund
    • , Peter Brzezinski
    •  & Christoph von Ballmoos

  • 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

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