Biophysics articles within Nature Communications

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  • Article
    | Open Access

    A bacterial export gate complex transports flagellar proteins across the cytoplasmic membrane, but the mechanism of this process is unclear. Here, the export gate complex is revealed as a proton–protein antiporter that uses separate components of the proton motive force for different steps of the export process.

    • Tohru Minamino
    • , Yusuke V. Morimoto
    •  & Keiichi Namba

  • Article
    | Open Access

    Cell-penetrating peptides can deliver molecular cargoes into living cells, and cross biological membranes by transduction—a non-endocytic mechanism. Here, the transduction efficiency of cyclic arginine-rich peptides is shown to be higher than that of more flexible linear peptides.

    • Gisela Lättig-Tünnemann
    • , Manuel Prinz
    •  & M. Cristina Cardoso

  • Article |

    The development of radial progenitor cells and astroglia in the cerebral cortex depends on the microtubule cytoskeleton. Eomet al. have developed a new mouse model where the microtubules of astrocytes and radial glia cells are fluorescently tagged, facilitating the detailed study of microtubule dynamics and development in these cells.

    • Tae-Yeon Eom
    • , Amelia Stanco
    •  & E.S. Anton

  • Article
    | Open Access

    How microtubules are organized correctly in plant cells is not well understood. Ambroseet al. use 4D imaging and computer modelling to show that sharp cell edges induce microtubule depolymerization and that the microtubule-associated protein CLASP mitigates this process to modulate array organization.

    • Chris Ambrose
    • , Jun F. Allard
    •  & Geoffrey O. Wasteneys

  • Article
    | Open Access

    RNA editing is important in regulating neuronal excitability, and a specific editing event has been shown to alter the permeation pathway of voltage-gate potassium channels. Gonzalezet al.find that the tip of the channel's inactivation gate makes a direct hydrophobic interaction with the edited position.

    • Carlos Gonzalez
    • , Angelica Lopez-Rodriguez
    •  & Miguel Holmgren

  • Article |

    Direct negative feedback decreases fluctuations in homoeostatic control, but intracellular regulatory systems are indirect. Here, an analytical expression is derived to show that indirect feedback in transcription and translation leads to more fluctuations for intermediate delays but not for long delays.

    • Andreas Grönlund
    • , Per Lötstedt
    •  & Johan Elf

  • Article |

    The inhibitor of apoptosis protein DIAP1 exists in an auto-inhibited conformation, but the details of its molecular interactions are poorly understood. Here, crystal structures reveal the auto-inhibition mechanism of DIAP1 and show how the active form of the protein binds to the effector caspase drICE.

    • Xiaochun Li
    • , Jiawei Wang
    •  & Yigong Shi

  • Article |

    Pagerank is widely used to rank web content; however, it is unknown how network topology affects its performance. The authors demonstrate that, in random networks, pagerank is sensitive to perturbations in topology, whereas scale-free networks contain a few super-stable nodes whose ranking is exceptionally stable.

    • Gourab Ghoshal
    •  & Albert-László Barabási

  • Article
    | Open Access

    von Willebrand factor (VWF) multimers mediate primary adhesion and aggregation of platelets. Jakobiet al. reveal a calcium-binding site in the VWF-A2 domain, and show that calcium binding encourages folding of the protein and has a role in mechanosensing.

    • Arjen J. Jakobi
    • , Alireza Mashaghi
    •  & Eric G. Huizinga

  • Article
    | Open Access

    Group-1 influenza A neuramidase proteins have a 150-cavity that can be targeted by drugs, but the 2009 H1N1 virus neuramidase is not thought to have a 150-cavity. Here, biophysical simulations show that the 2009 H1N1 neuramidase exists in solution with an open 150-cavity, which is stabilized by a salt bridge.

    • Rommie E. Amaro
    • , Robert V. Swift
    •  & Robin M. Bush

  • Article
    | Open Access

    Ambient levels of the neurotransmitter GABA tonically activate GABAA. Song et al.show that GABA can have both excitatory and inhibitory effects on hippocampal interneurons and find that low levels of GABA-mediated conductance are excitatory, whereas higher levels result in shunting inhibition.

    • Inseon Song
    • , Leonid Savtchenko
    •  & Alexey Semyanov

  • Article |

    Acoustic communication is important for the reproductive behaviour of frogs. Using acoustic playback experiments, Shenet al. show that calls from male concave-eared frogs (Odorrana tormota) evoke vocal responses and phonotaxis from females, but the females show no ultrasonic sensitivity.

    • Jun-Xian Shen
    • , Zhi-Min Xu
    •  & Shang-Chun Fan

  • Article |

    Class I anti-arrhythmic drugs act at cardiac sodium channels and are subdivided into classes Ia-c based on their effects on the electrocardiogram. Here, class Ib drugs are found to rely on cation–pi interactions for their activity, whereas class Ib and Ic drugs rely significantly less on this interaction.

    • Stephan A. Pless
    • , Jason D. Galpin
    •  & Christopher A. Ahern

  • Article |

    Undulating flight, an efficient mode of locomotion in flying birds, can theoretically also result in efficient locomotion in water. Here we demonstrate gait patterns resembling undulating flight in four marine vertebrate species comprising sharks and pinnipeds.

    • Adrian C. Gleiss
    • , Salvador J. Jorgensen
    •  & Rory P. Wilson

  • Article |

    Hydro-responsive plant movements have provided inspiration for the design of adaptive materials. Harringtonet al. investigate the hydration-dependent unfolding of ice plant seed capsules and find an origami-like folding pattern, which could aid the development of biomimetic folding structures.

    • Matthew J. Harrington
    • , Khashayar Razghandi
    •  & Ingo Burgert

  • Article |

    Encapsulating molecules within supramolecular frameworks for potential biological application is challenging. Bhatiaet al. incorporate a fluorescent polymer within an icosahedral DNA nanocapsule, and show that it can be used to target specific cells in vivoand map pH spatially and temporally.

    • Dhiraj Bhatia
    • , Sunaina Surana
    •  & Yamuna Krishnan

  • Article
    | Open Access

    The ability of synthetic amyloid β-protein to bind to prion proteins and alter synaptic plasticity has been previously reported. Here the relevance of this binding is investigated in brains of Alzheimer's disease patients and the interaction is shown to be blocked by antibodies to two distinct regions of prion proteins.

    • Darragh B. Freir
    • , Andrew J. Nicoll
    •  & John Collinge

  • Article
    | Open Access

    Two-dimensional fluid interfaces are ubiquitous, but studying their surface dynamic properties is difficult because of coupling between the film and bulk fluid. Choiet al.combine active microrheology with fluorescence microscopy to image fluid interfaces under applied stress.

    • S.Q. Choi
    • , S. Steltenkamp
    •  & T.M. Squires

  • Article
    | Open Access

    There is debate about the structural organization of the yeast centromeric nucleosome and the role of the nonhistone protein Scm3 in its assembly. Dechassaet al.find that yeast centromeric nucleosomes organize DNA in a left-handed superhelix, and show that Scm3 is a specific nucleosome assembly factor.

    • Mekonnen Lemma Dechassa
    • , Katharina Wyns
    •  & Karolin Luger

  • Article
    | Open Access

    The Q-cycle is thought to be an essential energetic component of the photosynthetic electron-transfer chain. Here, Chlamydomonas mutants with an inactive Q-cycle but normal levels ofb6fcomplexes are shown to display photosynthetic growth, demonstrating the dispensability of the Q-cycle in the oxygenic photosynthetic chain.

    • Alizée Malnoë
    • , Francis-André Wollman
    •  & Fabrice Rappaport

  • 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

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