Molecular conformation articles within Nature Communications

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  • Article
    | Open Access

    During protein elongation, the translocation of mRNA and tRNA molecules across the 30S ribosomal subunit is associated with large-scale motions of the 30S head domain. Here the authors carry out MD simulations to probe the associated steric interactions and identify novel tilting motions during the late stages of translocation.

    • Kien Nguyen
    •  & Paul C. Whitford

  • Article
    | Open Access

    The co-translational insertion of proteins into membranes requires interaction between a ribosome-bound signal recognition particle (SRP) and a membrane-bound translocon. Here the authors use cryo-EM and single particle reconstructions to obtain a comprehensive view of the co-translational protein targeting process.

    • Ahmad Jomaa
    • , Daniel Boehringer
    •  & Nenad Ban

  • Article
    | Open Access

    Asymmetric transport of auxin allows plants to orient growth of their roots towards gravity. Here, the authors show that the peptidyl-prolyl cis/transisomerase Pin1At contributes to root gravitropism and propose that it acts by altering the polarity of the PIN1 auxin transport protein.

    • Wanyan Xi
    • , Ximing Gong
    •  & Yih-Cherng Liou

  • Article
    | Open Access

    In response to intracellular signals, bacterial translational riboswitches embedded in mRNAs can regulate gene expression through inhibition of translation initiation. Here, the authors describe SiM-KARTS, a novel approach for detecting changes in the structure of single RNA molecules in response to a ligand.

    • Arlie J. Rinaldi
    • , Paul E. Lund
    •  & Nils G. Walter

  • Article
    | Open Access

    Intercellular signalling can be mediated by gap junction channels, and calcium blocks this signally during tissue injury. Here, the authors use X-ray crystallography and molecular dynamics to show that the calcium forms an electrostatic barrier to prevent transport of cations.

    • Brad C. Bennett
    • , Michael D. Purdy
    •  & Mark Yeager

  • Article
    | Open Access

    Bacterial type III secretion systems (T3SSs) inject virulence effector proteins into eukaryotic cells and are activated by host membrane contact. Here the authors report the in situ structure of the Chlamydia trachomatisT3SS in the presence or absence of host membrane, and observe compaction of the basal body embedded in the bacterial envelope.

    • Andrea Nans
    • , Mikhail Kudryashev
    •  & Richard D. Hayward

  • Article
    | Open Access

    The structure and biological properties of RNAs are a function of changing cellular conditions. Here, Baird et al.report a high-throughput Förster resonance energy transfer (FRET) method to rapidly compare RNA structure modulation by cognate and non-cognate ligands across multiplexed solution conditions.

    • Nathan J. Baird
    • , James Inglese
    •  & Adrian R. Ferré-D’Amaré

  • Article
    | Open Access

    NEK7, a kinase involved in mitosis, is regulated by the kinase NEK9. Here the authors identify the region in NEK9 that binds NEK7 and find that the mechanism of regulation involves dimerization coupled to structural changes in the active site.

    • Tamanna Haq
    • , Mark W. Richards
    •  & Richard Bayliss

  • Article
    | Open Access

    Single molecule super-resolution microscopy can reliably localize objects with high precision, but the accuracy can be called into question. Here the authors present a methodology to accurately and precisely measure nanometre separation and orientation of two fixed fluorophores from colour-separated images.

    • Kim I. Mortensen
    • , Jongmin Sung
    •  & James A. Spudich

  • Article
    | Open Access

    DNA supercoiling strongly affects its metabolism. By electron cryo-tomography, biochemical assays and molecular dynamics simulations, here the authors show that supercoiled DNA minicircles adopt unique and wide distributions of three-dimensional conformations, many with disrupted base pairs.

    • Rossitza N. Irobalieva
    • , Jonathan M. Fogg
    •  & Lynn Zechiedrich

  • Article
    | Open Access

    The calcium-regulated gelsolin family of actin-binding proteins includes adseverin. Here, the authors report the X-ray crystal structure of the N-terminal portion of adseverin and use small-angle scattering and molecular dynamics simulations to examine the calcium-dependent function of this protein.

    • Sakesit Chumnarnsilpa
    • , Robert C. Robinson
    •  & Cedric Leyrat

  • Article
    | Open Access

    Post-translational modification of histones has been implicated in gene regulation. Here, Lercher et al. generate synthetic GlcNAcylated histone 2A and nucleosomes and show that this modification can cause nucleosome destabilization, suggesting histone 2A O-GlcNAcylation may promote an open chromatin state and increase transcription.

    • Lukas Lercher
    • , Ritu Raj
    •  & Benjamin G. Davis

  • Article
    | Open Access

    Since their discovery more than fifty years ago, α-neurotoxins have been used to study acetylcholine receptor-coupled ion channels. Here, daCostaet al. find that toxin binding to a single site of the pentameric α7 receptor blocks function, suggesting the five binding sites are interdependent and the toxin arrests the sites in the inactive conformation.

    • Corrie J. B. daCosta
    • , Chris R. Free
    •  & Steven M. Sine

  • Article
    | Open Access

    Omecamtiv Mecarbil (OM) is a small molecule allosteric effector of cardiac myosin in clinical trials for treatment of systolic heart failure. Here the authors determine the crystal structure of an OM-bound human β-cardiac myosin motor domain to provide molecular level insight into the mechanism of drug action.

    • Donald A. Winkelmann
    • , Eva Forgacs
    •  & Ann M. Stock

  • Article
    | Open Access

    G protein-coupled receptors (GPCRs) are the largest family of transmembrane signaling proteins in humans and exhibit diverse activation mechanisms. Here, the authors combine electron microscopy, hydrogen deuterium exchange and Molecular dynamics simulations to gain insight into the activation mechanism of the glucagon receptor.

    • Linlin Yang
    • , Dehua Yang
    •  & Hualiang Jiang

  • Article
    | Open Access

    In biological systems, large pH-induced conformational changes can be observed in certain proteins, a phenomenon poorly understood at the molecular level. Here the authors describe a peptide with the ability to self-organize into either small or large nanotubes in a pH-dependent manner and detail the mechanism driving the transition.

    • Céline Valéry
    • , Stéphanie Deville-Foillard
    •  & Franck Artzner

  • Article
    | Open Access

    Depletion of calcium from intracellular stores induces interaction between the endoplasmic reticulum STIM1 protein and the plasma membrane ORAI1 channel that facilitates cellular calcium entry. Here Ma et al. characterize a STIM1 gain-of-function mutant and propose a conformational switch that controls ORAI1 gating.

    • Guolin Ma
    • , Ming Wei
    •  & Yubin Zhou

  • Article
    | Open Access

    Single molecule spectroscopy can visualise dynamic changes in protein conformation on the submillisecond timescale. Here, Otosu et al. apply two-dimensional fluorescence lifetime correlation spectroscopy to visualise dynamics between seven conformers of cytochrome con the microsecond timescale.

    • Takuhiro Otosu
    • , Kunihiko Ishii
    •  & Tahei Tahara

  • Article
    | Open Access

    Adenylate kinase (AdK) plays a key role in cellular energy homeostasis by catalysing the reversible magnesium-dependent formation of ADP from AMP and ATP. Here the authors present a detailed analysis of adenylate kinase’s conformational dynamics and characterize a high-energy state of AdK indispensable for catalysis.

    • Michael Kovermann
    • , Jörgen Ådén
    •  & Magnus Wolf-Watz

  • Article
    | Open Access

    The proteasome is a highly regulated complex fundamental for cell homeostasis and a target for cancer therapy. Here the authors use cryo-EM and single-particle analysis to obtain a detailed map of the interactions between each active sites of the core 20S proteasome and the irreversible inhibitor AdaAhx3L3VS.

    • Paula C.A. da Fonseca
    •  & Edward P. Morris

  • Article
    | Open Access

    The regulation of iron levels is an important physiological process as excess cellular iron is highly toxic. Here the authors present several structures of a bacterial ferric uptake regulator (Fur) in complex with the Fe2+transport protein operator and Fur box, shedding light on how iron promotes DNA recognition by Fur.

    • Zengqin Deng
    • , Qing Wang
    •  & Zhongzhou Chen

  • Article
    | Open Access

    EF-G enhances the rate of tRNA–mRNA translocation on the ribosome. Here the authors use single-molecule FRET to follow tRNA translocation in real time, identifying new chimeric intermediates and suggesting how EF-G binding and GTP hydrolysis change the energetic landscape of translocation to accelerate forward tRNA movement.

    • Sarah Adio
    • , Tamara Senyushkina
    •  & Marina V. Rodnina

  • Article |

    While active and inactive conformations of proteins have been characterised, pathways connecting these states remain largely obscure. Pontiggia et al.find that the inactive state of NtrC represents an ensemble of different conformers that interconvert to the active state via multiple pathways.

    • F. Pontiggia
    • , D.V. Pachov
    •  & D. Kern

  • Article
    | Open Access

    Type III restriction–modification enzymes consists of two methylation and one or two restriction subunits. Here the authors report the structure of the full EcoP15I complex bound to DNA, which suggests mechanisms for ATP hydrolysis dependent diffusion along DNA and how a dimeric methyltransferase modifies only one DNA strand.

    • Yogesh K. Gupta
    • , Siu-Hong Chan
    •  & Aneel K. Aggarwal

  • Article
    | Open Access

    The fundamental processes of protein insertion and translocation at the outer membrane are mediated by Omp85 proteins. Here the authors report structures of the translocase FhaC, showing that the critical L6 loop adopts a conformation similar to that of related insertases; establishing a common structural basis for Omp85 function.

    • Timm Maier
    • , Bernard Clantin
    •  & Vincent Villeret

  • Article
    | Open Access

    Whereas epidermal growth factor-induced dimerization is considered essential for EGFR signalling, the structurally related insulin receptor is a disulfide-linked dimer. Here the authors show that C. elegansEGFR is constitutively dimeric and undergoes subtle structural changes upon ligand binding that likely underlie allosteric activation.

    • Daniel M. Freed
    • , Diego Alvarado
    •  & Mark A. Lemmon

  • Article
    | Open Access

    The signal recognition particle plays a key role in the co-translational protein targeting of membrane and secretory proteins. Here the authors report a crystal structure of the ternary SRP complex in signal sequence bound and unbound forms, providing insight into how signal sequence binding is coupled to SRP receptor interaction.

    • Tobias Hainzl
    •  & A. Elisabeth Sauer-Eriksson

  • Article
    | Open Access

    Translation of mRNA into proteins is the least accurate process during genetic information transfer. Here the authors suggest—based on 11 high-resolution ribosome crystal structures—that the origin of protein missense errors involves molecular mimicry via tautomerism or ionization.

    • Alexey Rozov
    • , Natalia Demeshkina
    •  & Gulnara Yusupova

  • Article
    | Open Access

    The determination of RNA structures within high-molecular weight protein-RNA complexes in non-crystalline state is technically challenging. Here, the authors describe a solid-state NMR protocol for the determination of RNA structures at high resolution.

    • Alexander Marchanka
    • , Bernd Simon
    •  & Teresa Carlomagno

  • Article
    | Open Access

    DNMT1 is a methyl-transferase involved in maintaining tissue-specific patterns of DNA methylation. Here the authors solve the structure of a DNMT1-USP7 complex and demonstrate the mechanism by which DNMT1 stability is regulated through acetylation by preventing association with the deubiquitinase USP7.

    • Jingdong Cheng
    • , Huirong Yang
    •  & Yanhui Xu

  • Article
    | Open Access

    Ribosome stalling regulates gene expression by exposing otherwise inaccessible downstream ribosome-binding sites. Here the authors present a high-resolution Cryo-EM structure of the Bacillus subtilisMifM-stalled 70S ribosome to provide mechanistic insight into species-specific nascent peptide induced translational arrest.

    • Daniel Sohmen
    • , Shinobu Chiba
    •  & Daniel N. Wilson

  • Article
    | Open Access

    Spiegelmers are mirror-image oligonucleotide aptamers designed for therapeutic use. Here the authors describe the crystal structure of the mixed L-RNA/L-DNA Spiegelmer NOX-D20 bound to complement component C5a, a key mediator of the innate immune response and clinical target in acute and chronic inflammatory disorders.

    • Laure Yatime
    • , Christian Maasch
    •  & Axel Vater

  • Article
    | Open Access

    Localized chemical events such as the breakage of a bond between a protein and a ligand may trigger a global protein conformational change. Here, the authors use an X-ray free-electron laser to track the motion of myoglobin in response to photoinduced ligand release, and observe a picosecond proteinquake.

    • Matteo Levantino
    • , Giorgio Schirò
    •  & Marco Cammarata

  • Article |

    Lysosomal phospholipase A2 (LPLA2) and lecithin:cholesterol acyltransferase (LCAT) are important lipid metabolizing enzymes. Here the authors present crystal structures of LPLA2 and LCAT that reveal the unique architecture of this small family of enzymes involved in human physiology and disease.

    • Alisa Glukhova
    • , Vania Hinkovska-Galcheva
    •  & John J. G. Tesmer

  • Article |

    The bacterial Hsp70 chaperone system consists of DnaJ, DnaK and GrpE. To understand how these chaperones cooperate, Nunes et al. monitor refolding immunoglobulin domains using single-molecule force microscopy to demonstrate that the ‘holdase’ DnaJ can show foldase activity and suggest that GrpE can facilitate substrate release from DnaK.

    • João M. Nunes
    • , Manajit Mayer-Hartl
    •  & Daniel J. Müller

  • Article |

    Ramachandran plots are a convenient means of describing protein backbone conformation by depicting the distribution of Ca bond rotations. Here, the authors devise an alternative descriptor based on hydrogen bond rotations, and apply it to describe protein structures using a vocabulary of 30 hydrogen-bonding motifs.

    • Robert C. Penner
    • , Ebbe S. Andersen
    •  & Jørgen E. Andersen

  • Article |

    Twisters ribozymes are a recently discovered class of non-coding, site-specific self-cleaving RNAs. Here Ren et al. describe a crystal structure of the env22twister ribozyme, propose an ion coordination and catalytic mechanism, and contrast their findings with those of two recently reported twister structures.

    • Aiming Ren
    • , Marija Košutić
    •  & Dinshaw J. Patel

  • Article |

    Abl is a cytoplasmic tyrosine kinase important for growth, whose hyper activation is associated with several types of cancers. Here, the authors use recombinant Abl protein to uncover the molecular mechanism underlying allosteric activation of Abl by its SH2 domain through the regulation of autophosphorylation.

    • Allan Joaquim Lamontanara
    • , Sandrine Georgeon
    •  & Oliver Hantschel

  • Article |

    Voltage-gated sodium channels (Nav) are transmembrane proteins that underlie action potentials in excitable tissues. Here, Gabelli et al. suggest a novel mechanism for the cytoplasmic control of switching from the inactivated to the non-inactivated form of the Nav1.5 channel that involves dimerization.

    • Sandra B. Gabelli
    • , Agedi Boto
    •  & L. Mario Amzel

  • 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 |

    At cell–cell adhesions, α-catenin contains a cryptic vinculin-binding site. Here, Yao et al. demonstrate, using magnetic tweezers, that physiologically relevant forces unfurl α-catenin to reveal the vinculin-binding site, and allow the reversible binding of vinculin to mechanically reinforce the adhesion.

    • Mingxi Yao
    • , Wu Qiu
    •  & Jie Yan

  • 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

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