Biophysics articles within Nature Communications

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  • Article |

    The detailed interactions of membrane proteins with their lipid environment are poorly understood. Sonntaget al. use low-resolution X-ray crystallographic data and molecular dynamics simulations to study the manner in which the sarcoendoplasmic reticulum Ca2+–ATPase adapts to different membrane environments.

    • Yonathan Sonntag
    • , Maria Musgaard
    •  & Lea Thøgersen

  • Article |

    Little is known about the effects of molecular crowding and confinement on biomolecule function. Castronovoet al. investigate the reactions of restriction enzymes with DNA confined in bushy matrices and find that the enzymes enter at the side of the matrix before diffusing two-dimensionally.

    • Matteo Castronovo
    • , Agnese Lucesoli
    •  & Giacinto Scoles

  • Article |

    N-methyl-D-aspartate receptors mediate excitatory synaptic transmission, and those containing GluN2D subunits have an unusually long deactivation time. Vance et al. show that the conformational variability of the ligand-binding domain and the structure of the activating ligand influence deactivation time.

    • Katie M. Vance
    • , Noriko Simorowski
    •  & Hiro Furukawa

  • Article |

    The spinal V2a interneurons control left–right limb alternation during mouse locomotion, but only at high frequencies. In this study, the authors show that only half of these neurons are active during locomotion, and that they receive increasing synaptic drive to increase their activity as locomotion accelerates.

    • Guisheng Zhong
    • , Kamal Sharma
    •  & Ronald M. Harris-Warrick

  • Article
    | Open Access

    Eukaryotic cell plasma membranes possess a mechanism to repair tears caused by stimuli such as mechanical stress. The authors demonstrate that annexin-A5, when assembled into two-dimensional arrays in the presence of calcium, is required for membrane repair.

    • Anthony Bouter
    • , Céline Gounou
    •  & Alain R. Brisson

  • Article
    | Open Access

    Deubiquitinating enzymes are involved in multiple cellular processes, including cell viability. The authors reveal a role for the deubiquitinating enzyme, USP17, in the migration of cells in response to chemokines and show that USP17 is required for the relocalization of GTPases involved in cell motility.

    • Michelle de la Vega
    • , Alyson A. Kelvin
    •  & James A. Johnston

  • Article |

    The formation of hydrophilic protein–protein interactions cannot be explained by charge–charge interactions. Here, molecular simulations reveal that water forms an adhesive hydrogen-bonded network between proteins, stabilizing intermediate states before the bound complex forms.

    • Mazen Ahmad
    • , Wei Gu
    •  & Volkhard Helms

  • Article |

    Single-molecule force spectroscopy is used to study single molecule interactions, but probing short-lived events is difficult. Here, a nanomechanical interface is developed, which allows the study of microsecond timescale interactions.

    • Mingdong Dong
    •  & Ozgur Sahin

  • Article
    | Open Access

    Lipid phosphodiesters affect the conformation of certain potassium channels, but the details of the lipid-channel interactions are unclear. Here, the KvAP channel is found to switch from an active to a resting state when the channels are transferred from a phospholipid membrane to a bilayer lacking phosphodiesters.

    • Hui Zheng
    • , Weiran Liu
    •  & Qiu-Xing Jiang

  • Article |

    Glutamate is the major excitatory neurotransmitter in the mammalian nervous system. Here, a glutamate receptor is reported that has properties intermediate to those of bacterial and eukaryotic glutamate-gated ion channels, suggesting a link in the evolution of ionotropic glutamate receptors.

    • H. Janovjak
    • , G. Sandoz
    •  & E. Y. Isacoff

  • Article |

    The cochlear amplifier in the inner ear is thought to mediate sensitivity to soft sounds, but this power gain has not been measured directly. Renet aluse an interferometer to measure the volume displacement and velocity of the cochlear partition and demonstrate experimentally that the cochlea amplifies soft sounds.

    • Tianying Ren
    • , Wenxuan He
    •  & Peter G. Gillespie

  • Article |

    Seahorses evolved from pipefish, which have a remarkably different body shape. Here, by examining seahorse feeding behaviour and using a mathematical model, Van Wassenberghet al. demonstrate that the head, neck and trunk posture of the seahorse allows for the effective capture of their prey.

    • Sam Van Wassenbergh
    • , Gert Roos
    •  & Lara Ferry

  • Article
    | Open Access

    The gastric proton pump, H+,K+-ATPase, contributes to stomach acidification and is a target of acid suppressants. Here, the three-dimensional structure of the pump is determined using electron crystallography, providing the first structural information about the binding of a new class of acid suppressants.

    • Kazuhiro Abe
    • , Kazutoshi Tani
    •  & Yoshinori Fujiyoshi

  • Article
    | Open Access

    Deformations in nanocrystals smaller than 10 nm are not well understood. The authors perform compression high-resolution transmission electron microscopy studies of gold nanoparticles, and determine that the nanoparticles deform through the emission of partial dislocations from free surfaces.

    • He Zheng
    • , Ajing Cao
    •  & Scott X. Mao

  • Article |

    Materials such as rubber tend to soften when cyclically deformed. Here, however, the authors find that bundled actin networks can show cyclic hardening and retain a memory of the maximum strain they have been subjected to.

    • K. M. Schmoller
    • , P. Fernández
    •  & A. R. Bausch

  • Article
    | Open Access

    γ-Secretase modulators have promise in the treatment of Alzheimer's disease, but their molecular target is uncertain. Here, fluorescence resonance energy transfer is used to determine that the γ-secretase allosteric site is within the γ-secretase complex and that substrate docking is required for modulators to access the site.

    • Kengo Uemura
    • , Katherine C. Farner
    •  & Oksana Berezovska

  • Article |

    Fusion proteins containing blue-light-activated domains have been used as molecular switches to investigate cell signalling, but molecular understanding of the transduction pathway is lacking. Here, MD simulations are used to elucidate the transduction mechanism in a light oxygen voltage2-Ja photosensor.

    • Emanuel Peter
    • , Bernhard Dick
    •  & Stephan A. Baeurle

  • Article
    | Open Access

    Mutation of theTectbgene reduces auditory sensitivity but increases frequency selectivity. Here the authors show that Tectb mutation reduces both the spatial and temporal propagation of travelling waves along the tectorial membrane, explaining the unexpected auditory abnormalities in this mutant.

    • Roozbeh Ghaffari
    • , Alexander J. Aranyosi
    •  & Dennis M. Freeman

  • Article |

    Protein interactions in biological environments are expected to differ from the situationin vitro. In this study, a thermophoresis-based technique is described that allows the analysis of protein and small-molecule interactions in biological liquids; the work may allow more efficient drug development.

    • Christoph J. Wienken
    • , Philipp Baaske
    •  & Stefan Duhr

  • Article
    | Open Access

    Frataxin is an essential protein that has been linked to iron–sulphur cluster assembly, and reduced levels are associated with Friedrich's ataxia. In this study, a combination of techniques is used to probe the interactions of the bacterial frataxin orthologue CyaY with the iron–sulphur cluster assembly machinery.

    • Filippo Prischi
    • , Petr V. Konarev
    •  & Annalisa Pastore

  • Article |

    SNARE protein-mediated vesicle fusion is usually monitored by indirect lipid mixing. Diaoet al. have developed a FRET-based single-vesicle content mixing assay, which elucidates fusion pore formation, and shows that the yeast SNARE complex mediates pore expansion in the absence of accessory proteins.

    • Jiajie Diao
    • , Zengliu Su
    •  & Taekjip Ha

  • Article
    | Open Access

    A recent X-ray structure revealed the closed state of a P2X receptor ion channel. Here, Li and colleagues probe the structural rearrangements that take place during channel opening by measuring the effects of covalent modification of engineered cysteines.

    • Mufeng Li
    • , Toshimitsu Kawate
    •  & Kenton J. Swartz

  • Article |

    To ensure correct cell division Staphylococci must remember which plane they previously divided along, but the mechanism by which this is achieved is unclear. In this article, using atomic force microscopy, peptidoglycan ribs are reported to mark previous planes of division.

    • Robert D. Turner
    • , Emma C. Ratcliffe
    •  & Simon J. Foster

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