Molecular conformation articles within Nature

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  • Article |

    High-speed atomic force microscopy single-molecule imaging and cryo-EM analysis discover and reveal the structure of a TRPV3 pentamer, providing evidence for a non-canonical pentameric TRP-channel assembly, laying the foundation for new directions in TRP channel research.

    • Shifra Lansky
    • , John Michael Betancourt
    •  & Simon Scheuring

  • Article |

    Through the use of cryo-electron microscopy and molecular dynamics stimulations, mechanistic insight into the binding of an odorant to the human odorant receptor OR51E2 is provided.

    • Christian B. Billesbølle
    • , Claire A. de March
    •  & Aashish Manglik

  • Article |

    Cryo-electron microscopy and high-speed atomic force microscopy reveal that PIEZO1 can reversibly deform its shape towards a planar structure, which may explain how the PIEZO1 channel is gated in response to mechanical stimulation.

    • Yi-Chih Lin
    • , Yusong R. Guo
    •  & Simon Scheuring

  • Letter |

    Cryo-electron microscopy structures of two stoichiometries of heteromeric acetylcholine receptors in complex with nicotine reveal principles of subunit assembly and the structural basis of the distinctive biophysical and pharmacological properties of the different stoichiometries.

    • Richard M. Walsh Jr
    • , Soung-Hun Roh
    •  & Ryan E. Hibbs

  • Letter |

    The near-complete in vitro reconstitution of the mitotic spindle assembly checkpoint reveals how the assembly of its effector, the mitotic checkpoint complex, is catalysed.

    • Alex C. Faesen
    • , Maria Thanasoula
    •  & Andrea Musacchio

  • Article |

    dG•dT and rG•rU ‘wobble’ mispairs in DNA and RNA transiently form base pairs with Watson–Crick geometry via tautomerization and ionization with probabilities that correlate with misincorporation probabilities during replication and translation.

    • Isaac J. Kimsey
    • , Katja Petzold
    •  & Hashim M. Al-Hashimi

  • News & Views |

    Some of the principles underlying how amino-acid sequences determine the three-dimensional structures of proteins have been defined. This has enabled a successful approach to designing protein folds from scratch. See Article p.222

    • Birte Höcker

  • Article |

    This study develops an NMR-based approach that can capture previously inaccessible, highly transient, low-populated ‘excited states’ in RNA; the localized rearrangements in base-pairing giving rise to these states are found to affect function by changing the exposure of residues required for a specific biological process.

    • Elizabeth A. Dethoff
    • , Katja Petzold
    •  & Hashim M. Al-Hashimi

  • Letter |

    A complex of RNA and protein known as the box C/D RNP catalyses the site-specific modification of RNAs with a 2′-O-methylation group. The structure of the full complex has now been solved, including the guide RNA and either of two substrate RNAs. This structure reveals how the guide and target RNAs are aligned, and how the methyltransferase subunit, fibrillarin, facilitates placement of the target ribose into the active site.

    • Jinzhong Lin
    • , Shaomei Lai
    •  & Keqiong Ye

  • Letter |

    The X-ray crystal structure of the human β2 adrenergic receptor, a G-protein-coupled receptor (GPCR), covalently bound to a small-molecule agonist is solved. Comparison of this structure with structures of this GPCR in an inactive state and in an antibody-stabilized active state reveals how binding events at both the extracellular and intracellular surfaces stabilize the active conformation of the receptor. Molecular dynamics simulations suggest that the agonist-bound active state spontaneously relaxes to an inactive-like state in the absence of a G protein.

    • Daniel M. Rosenbaum
    • , Cheng Zhang
    •  & Brian K. Kobilka

  • Letter |

    The anomeric effect is a chemical phenomenon that refers to an observed stabilization of six-membered carbohydrate rings when they contain an electronegative substituent at the C1 position of the ring. This stereoelectronic effect influences the three-dimensional shapes of many biological molecules, but the underlying physical origin is unclear. Here it is shown that complexes formed between a truncated peptide motif and an isolated sugar in the gas phase are nearly identical structurally; however, the strength of the polarization of their interactions with the peptide differs greatly. It will be important to re-evaluate the influence, and biological effects, of substituents at position C2 of the six-membered carbohydrate rings.

    • Emilio J. Cocinero
    • , Pierre Carcabal
    •  & Benjamin G. Davis

  • Letter |

    During translation, tRNAs enter the ribosome and then move sequentially through three sites, known as A, P and E, as they transfer their attached amino acids onto the growing peptide chain. How the ribosome facilitates tRNA translocation between the sites remains largely unknown. Now a study uses multiparticle cryoelectron microscopy of a ribosome bound to the translation elongation factor, EF-G, to get information about tRNA movement. It identifies two new substates and sees that translocation is linked to unratcheting of the 30S ribosomal subunit.

    • Andreas H. Ratje
    • , Justus Loerke
    •  & Christian M. T. Spahn

  • Letter |

    The E1 and E2 glycoproteins of alphaviruses form heterodimers and assemble into spikes on the virus surface, which mediate receptor binding and endocytosis. When the virion encounters acidic pH in the endosome E1 and E2 dissociate and E1 triggers fusion with the endosomal membrane. Two papers now provide the first crystal structures for glycoprotein complexes incorporating E2 at acidic and neutral pH, respectively. Together they provide insight into how fusion activation is controlled in alphaviruses.

    • James E. Voss
    • , Marie-Christine Vaney
    •  & Félix A. Rey

  • Letter |

    In Escherichia coli, the uptake of L-fucose, an important source of carbon for microorganisms, is mediated by a proton symporter from the major facilitator superfamily (MFS). These authors report the first X-ray crystal structure of the outward-open conformation of an MFS proton transporter, FucP. Building on previous work, they develop a working model for how the substrate is recognized by the transporter and how the protein mediates L-fucose/proton symport.

    • Shangyu Dang
    • , Linfeng Sun
    •  & Nieng Yan

  • Letter |

    Transporter proteins from the MATE (multidrug and toxic compound extrusion) family are involved in metabolite transport in plants, and in multiple-drug resistance in bacteria and mammals. Here, the X-ray crystal structure of a MATE transporter from Vibrio cholerae is reported. The structure is in an outward-facing conformation, and reveals a cation-binding site near to residues previously deemed essential for transport.

    • Xiao He
    • , Paul Szewczyk
    •  & Geoffrey Chang

  • Letter |

    Normally, expression of bacterial DNA damage repair genes is repressed by the binding of LexA protein to SOS ‘boxes’ in their operators. DNA damage activates the RecA protein, which promotes autocleavage of LexA such that its repression is relieved and repair proteins are expressed. These authors solve several structures of LexA dimer bound to SOS box DNA, and find that the orientation of the DNA-binding wings can account for the strict intersite spacing.

    • Adrianna P. P. Zhang
    • , Ying Z. Pigli
    •  & Phoebe A. Rice

  • Letter |

    The bacterial flagellar motor drives the rotation of flagellar filaments, propelling bacteria through viscous media. The rotation can switch from an anticlockwise to a clockwise direction, determining a smooth or tumbling motion. A protein called FliG forms a ring in the motor's rotor, and has been proposed to adopt distinct conformations that induce switching. Here, the full-length structure of FliG is presented, and conformational changes are identified that are involved in switching between clockwise and anticlockwise rotations.

    • Lawrence K. Lee
    • , Michael A. Ginsburg
    •  & Daniela Stock

  • Article |

    During protein synthesis within the ribosome, transfer RNAs (tRNAs) move sequentially through different sites as their attached amino acids are transferred onto the growing protein chain. Large conformational movements accompany this process. Here, a staggering 1.9 million electron cryomicroscopy images of the ribosome have been processed to visualize these changes. The results reveal that the ribosome functions as a Brownian machine that couples spontaneous changes driven by thermal energy to directed movement.

    • Niels Fischer
    • , Andrey L. Konevega
    •  & Holger Stark

  • Letter |

    XXXMicrotubules are nucleated in vivo by γ-tubulin complexes and comprise 13 protofilaments. How this precise geometry is controlled remains unclear. These authors report the cryo-electron microscopic structure of the universally conserved, core microtubule nucleating complex, γ-tubulin small complex. The structure provides insight into how this complex establishes thirteen-fold tubulin symmetry.

    • Justin M. Kollman
    • , Jessica K. Polka
    •  & David A. Agard

  • Letter |

    Large-conductance Ca2+-gated K+ (BK) channels are essential for many biological processes, such as smooth muscle contraction and neurotransmitter release. Here, the X-ray crystal structure is presented of the entire cytoplasmic region of the human BK channel in a Ca2+-free state. Moreover, a voltage-gated K+ channel pore of known structure is 'docked' onto the gating ring to generate a structural model for the full BK channel.

    • Yunkun Wu
    • , Yi Yang
    •  & Youxing Jiang

  • News & Views |

    Membrane transporter proteins switch between conformational states to move substrates across membranes. The transition between these states can now be studied using single-molecule experiments.

    • Nathan K. Karpowich
    •  & Da-Neng Wang

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