Structural biology articles within Nature Communications

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  • Article
    | Open Access

    Cofactor-mediated energy and electron transfer in photosystem II occurs preferentially through one branch of the reaction centre, despite there being a symmetric path available. Here, the authors use computational methods to determine the influence of protein conformation on this selectivity.

    • Lu Zhang
    • , Daniel-Adriano Silva
    •  & Xuhui Huang

  • 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 HOP2-MND1 heterodimer is essential for homologous recombination. Here, Bugreev et al. analyse its mechanism of action in vitroand show that HOP2-MND1 stabilizes an active conformation of Rad51, thus triggering DNA strand exchange.

    • Dmitry V. Bugreev
    • , Fei Huang
    •  & Alexander V. Mazin

  • Article |

    The transfer of a phosphate group from a CDP-linked donor to an acceptor alcohol is catalysed by CDP-alcohol phosphotransferases. Here, Sciara et al. report crystal structures of a CDP-alcohol phosphotransferase, define roles of conserved residues and propose a mechanism of action for this protein family.

    • Giuliano Sciara
    • , Oliver B. Clarke
    •  & Filippo Mancia

  • 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 |

    α-synuclein is a protein whose aberrant aggregation is associated with Parkinson’s disease. Here, Fusco et al.characterize α-synuclein bound to lipid membranes using a combination of solution and solid-state NMR spectroscopy and provide insights into the molecular processes associated with the aggregation of this protein.

    • Giuliana Fusco
    • , Alfonso De Simone
    •  & Gianluigi Veglia

  • Article
    | Open Access

    Cell–cell fusion in Caenorhabditis elegans is mediated by EFF-1 and AFF-1 proteins. Here, the authors present an electron cryomicroscopy 3D reconstruction of EFF-1 in the membrane, and combine snapshots of membrane fusion in vitrowith a recently reported crystal structure to propose a mechanism for the fusion process.

    • Tzviya Zeev-Ben-Mordehai
    • , Daven Vasishtan
    •  & Kay Grünewald

  • Article
    | Open Access

    Eukaryotic Initiation Factor 2 (eIF2) initiates protein synthesis aided by its partner eIF2B, which stimulates guanine nucleotide exchange on eIF2. Here, Gordiyenko et al. show that eIF2B exists as a decamer and propose a model for its subunit arrangement that provides new insight into its function.

    • Yuliya Gordiyenko
    • , Carla Schmidt
    •  & Carol V. Robinson

  • Article |

    The peptidoglycan hydrolase PcsB is required for cell wall splitting during cell division in Streptococci. Bartual et al.show that PcsB adopts an autoinhibited dimeric structure, and demonstrate the muralytic activity of the uninhibited catalytic domain.

    • Sergio G. Bartual
    • , Daniel Straume
    •  & Juan A. Hermoso

  • Article |

    The astrocytic vesicular protein, synaptobrevin2 (Sb2), is implicated in neurotransmitter release, but its vesicular arrangement is poorly understood. Here, Singh et al. use super-resolution fluorescence microscopy to show that the total number of endogenous Sb2 molecules per vesicle is ≤25.

    • Priyanka Singh
    • , Jernej Jorgačevski
    •  & Robert Zorec

  • Article
    | Open Access

    In the malarial parasitophorous vacuole, the serine protease SUB1 processes parasite proteins that are required for release from host cells and invasion. Here, the authors report the first crystallographic structure of SUB1 in complex with its cognate prodomain revealing its substrate interactions and providing insight into its regulation.

    • Chrislaine Withers-Martinez
    • , Malcolm Strath
    •  & Michael J. Blackman

  • Article |

    Frameshift mutations in the protein polyglutamine tract-binding protein 1 (PQBP1) are believed to cause X-linked mental retardation. Here, Mizuguchi et al.present the crystal structure of a C-terminal fragment of PQBP1 in complex with the spliceosomal protein U5–15kD, and show details of this interaction that can lead to mechanistic insights into the disease.

    • Mineyuki Mizuguchi
    • , Takayuki Obita
    •  & Hitoshi Okazawa

  • Article |

    The binding affinity of a protein for its ligand is governed by the rates of ligand association and dissociation. Here the authors show that intrinsic conformational dynamics of maltose binding protein dictate the ligand dissociation rate, and hence the affinity of the protein for maltose.

    • Moon-Hyeong Seo
    • , Jeongbin Park
    •  & Hak-Sung Kim

  • 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 |

    The nuclear receptor PPARγ regulates insulin sensitivity and is the molecular target of anti-diabetic drugs. Here, Hughes et al. show demonstrate binding of synthetic PPARγ agonists to a previously unknown binding site within PPARγ and show this affects structure and function of the receptor.

    • Travis S. Hughes
    • , Pankaj Kumar Giri
    •  & Douglas J. Kojetin

  • Article
    | Open Access

    Type II PI4-kinase dysfunction is associated with diseases including cancer and Alzheimer's disease; however, the development of specific modulators has been hampered by a lack of structural information. Zhou et al. present the crystal structure of PI4KIIα in its ADP-bound form, providing insight into its regulation.

    • Qiangjun Zhou
    • , Jiangmei Li
    •  & Chang Chen

  • Article
    | Open Access

    Cyclin-dependent kinase 12 (Cdk12) phosphorylates the C-terminal domain (CTD) of RNA polymerase II to regulate transcription. Here, the authors solve the crystal structure of the Cdk12 kinase domain and show that Cdk12 has its highest activity on a CTD substrate that carries a serine 7 phosphorylation.

    • Christian A. Bösken
    • , Lucas Farnung
    •  & Matthias Geyer

  • Article |

    Our understanding of ribosome biogenesis is limited by a lack of structural knowledge of assembly intermediates. Here, Leidig et al.report a high-resolution cryo-EM structure of a pre-60S particle that suggests that substantial rearrangements of the 5S RNP are required during ribosome maturation.

    • Christoph Leidig
    • , Matthias Thoms
    •  & Roland Beckmann

  • Article |

    Activation of c-src kinase is associated with uncontrolled growth and metastasis of tumour cells. Shukla et al.model conformational changes in c-src during activation, and identify an allosteric site in an intermediate state that may provide a target for small molecule therapeutics.

    • Diwakar Shukla
    • , Yilin Meng
    •  & Vijay S. Pande

  • Article |

    Crystallographic studies have shown that non-NMDA glutamate receptors exhibit fourfold symmetry in the transmembrane domain in the closed state; however, structural data regarding channel opening is lacking. Using chimeric receptors, Wilding et al.provide evidence that this fourfold symmetry is maintained in the open state.

    • Timothy J. Wilding
    • , Melany N. Lopez
    •  & James E. Huettner

  • Article |

    Serial femtosecond X-ray crystallography permits the use of very small protein crystals; however, a continuous flow of sample is required. Weierstall et al. design and demonstrate an injector system that can supply microcrystals in the lipidic cubic phase, dramatically reducing the quantities of protein required.

    • Uwe Weierstall
    • , Daniel James
    •  & Vadim Cherezov

  • Article |

    Bacterial two-component systems relay extracellular signals to transcriptional networks via response regulators. Narayanan et al.present structures of the response regulator KdpE bound to DNA, and show that asymmetric interactions between the receiver and DNA-binding domains are required to sustain gene expression.

    • Anoop Narayanan
    • , Shivesh Kumar
    •  & Dinesh A. Yernool

  • Article
    | Open Access

    The structural heterogeneity of a biomolecular crystal structure is typically captured using atomic B-factors, determined during structure refinement. Here, the authors use molecular dynamics to show that this strategy is flawed, and that crystallographic B-factors underestimate structural heterogeneity.

    • Antonija Kuzmanic
    • , Navraj S. Pannu
    •  & Bojan Zagrovic

  • Article |

    The phosphorylation of proteins is a common mechanism for signal transduction. Here, the authors present a structural analysis of a histidine kinase in the process of autophosphorylation, helping to elucidate the catalytic mechanism.

    • Patricia Casino
    • , Laura Miguel-Romero
    •  & Alberto Marina

  • Article
    | Open Access

    The molecular determinants underlying ligand gating of cyclic nucleotide-modulated ion channels remain unclear. Kowal et al.determine the conformational changes underlying cAMP binding to the bacterial channel MloK1, and propose a mechanism for coupling of ligand gating and voltage sensing in eukaryotic HCN channels.

    • Julia Kowal
    • , Mohamed Chami
    •  & Henning Stahlberg

  • Article
    | Open Access

    Microtubules are tubes in which helical symmetry is broken at a single ‘A-lattice’ seam. Katsuki et al.show that microtubules containing additional A-lattice seams exhibit decreased stability, and propose that such seams may act as trigger points for microtubule catastrophe.

    • Miho Katsuki
    • , Douglas R. Drummond
    •  & Robert A. Cross

  • Article |

    Protein allosteric interactions involve a transfer of structural changes to a remote site. Here, the authors study the relationship between allosteric binding and energy flow, showing how the energy transport mechanism conveys binding energy to remote sites.

    • Guifeng Li
    • , Donny Magana
    •  & R. Brian Dyer

  • Article
    | Open Access

    Kinetochores must interact with both polymerizing (straight) and depolymerizing (curved) microtubules to ensure correct mitotic chromosome segregation. Abad et al. reveal how this flexibility is achieved through structural characterization of the interactions between microtubules and the kinetochore protein Ska1.

    • Maria Alba Abad
    • , Bethan Medina
    •  & A. Arockia Jeyaprakash

  • Article |

    Proteins that are translocated across the endoplasmic reticulum (ER) membrane may be subject to glycosylation during transport. Using cryoelectron microscopy of native ER membranes, Pfeffer et al.map the location of oligosaccharyl-transferase within the translocon, providing insight into how these processes are coupled.

    • Stefan Pfeffer
    • , Johanna Dudek
    •  & Friedrich Förster

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