Biophysics articles within Nature Communications

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  • Article
    | Open Access

    Single-molecule force spectroscopy provides useful quantitative information about the properties of macromolecules. Otto and colleagues non-invasively inspect the tension dynamics in a taut strand of DNA, thereby extending the use of single-molecule force spectroscopy to the study of macromolecular dynamics.

    • Oliver Otto
    • , Sebastian Sturm
    •  & Klaus Kroy

  • Article
    | Open Access

    Voltage-gated potassium channels cycle between closed and open states through poorly-defined transitions. Pless and colleagues incorporate artificial amino acids into Shaker potassium channels and find that that the negative electrostatic surface potential of Phe481, destabilizes the channel open state.

    • Stephan A. Pless
    • , Ana P. Niciforovic
    •  & Christopher A. Ahern

  • Article
    | Open Access

    The coffee ring effect is commonly observed in drying droplets containing suspended matter leading to a deposition at the droplet edge. Sempels et al. show that self-generated biosurfactants in living bacterial systems reverse the coffee ring effect and result in a homogeneous deposition.

    • Wouter Sempels
    • , Raf De Dier
    •  & Jan Vermant

  • Article
    | Open Access

    IP39 is an abundant protozoan protein known to form highly-ordered striations in Euglena gracilis’ plasma membrane. Here, Suzuki et al. determine its three-dimensional structure by electron crystallography revealing that IP39 polymerises to form trimeric longitudinal units arranged in a molecular strand of antiparallel double-rows.

    • Hiroshi Suzuki
    • , Yasuyuki Ito
    •  & Sachiko Tsukita

  • Article |

    Electrophysiological studies in some fish species suggest that proprioception is needed for fin movement. Here the authors test mechanosensory abilities of afferent nerves in pectoral fin rays, and find that the activity of fin ray nerve fibres reflects the amplitude and velocity of fin ray bending.

    • Richard Williams IV
    • , Nicole Neubarth
    •  & Melina E. Hale

  • Article |

    Alcohols and anaesthetics exert their effects by potentiating ligand-gated ion channels. Here, the authors determine crystal structures of a bacterial ligand-gated ion channel in the presence of alcohols and anaesthetics, and describe a structural mechanism for stabilization of the open form of the channel.

    • Ludovic Sauguet
    • , Rebecca J. Howard
    •  & Marc Delarue

  • Article
    | Open Access

    Bone is a natural composite of collagen and hydroxyapatite but, surprising, little is known about its characteristics at the molecular scale. Nair et al. conduct molecular-scale simulations of mineralized collagen networks to better understand how bone achieves superior mechanical properties to its constituents.

    • Arun K. Nair
    • , Alfonso Gautieri
    •  & Markus J. Buehler

  • Article |

    Ribosomal protein synthesis is driven by the hydrolysis of GTP. Wallin and colleagues employ molecular dynamics and computer simulations to show that a universally conserved histidine promotes GTP hydrolysis in its protonated form, and is driven into the active conformation by interactions with the ribosome.

    • Göran Wallin
    • , Shina C. L. Kamerlin
    •  & Johan Åqvist

  • Article |

    Light-driven proton-pumping rhodopsins are widely distributed in microorganisms and convert sunlight energy into proton gradients. Inoue et al. report the discovery of a light-driven sodium ion pump from marine bacteria.

    • Keiichi Inoue
    • , Hikaru Ono
    •  & Hideki Kandori

  • Article |

    Transcription factor diffusion along DNA regulates many fundamental cellular and developmental processes. Kaur et al. combine photoactivation and fluorescence correlation spectroscopy to investigate transcription factor diffusion in mouse embryos and show that diffusion kinetics change during cell differentiation.

    • Gurpreet Kaur
    • , Mauro W. Costa
    •  & Nicolas Plachta

  • Article |

    Cullin 1-RING ubiquitin ligase complexes interact with a wide variety of substrates by recruiting different substrate receptor subunits. Here the authors demonstrate that CAND1 promotes rapid exchange of substrate receptors, thus ensuring comprehensive sampling of the entire repertoire.

    • Shuangding Wu
    • , Wenhong Zhu
    •  & Dieter A. Wolf

  • Article |

    Macromolecular crowding significantly affects interactions between macromolecules such as proteins, DNA and RNA. Akabayov and colleagues use a SAXS reconstitution assay to show that the effect of macromolecular crowding on T7 DNA replication causes structural changes of the replisome.

    • Barak Akabayov
    • , Sabine R. Akabayov
    •  & Charles C. Richardson

  • Article |

    The bacterial tetracycline resistance protein Tet(O) binds to the ribosome, preventing tetracycline from inhibiting translation. Using cryo-electron microscopic reconstruction, the authors present an atomic model of Tet(O) bound to the 70S ribosome, and reveal how Tet(O) promotes antibiotic resistance.

    • Wen Li
    • , Gemma C. Atkinson
    •  & Joachim Frank

  • Article
    | Open Access

    In outwardly rectifying potassium channels, depolarization initiates conformational changes in voltage-sensing domains. Goldschen-Ohmet al. find that movement of three specific domains correlates with conductance levels, and rearrangements of a fourth domain results in preinactivation subconductance states.

    • Marcel P. Goldschen-Ohm
    • , Deborah L. Capes
    •  & Baron Chanda

  • Article
    | Open Access

    RNase P is a key enzyme implicated in transfer RNA maturation that removes the 5′-leader sequences from transfer RNA precursors. In this study, a biophysical characterization of a novel protein-only variant of RNase P, known as PRORP (PROteinaceous RNase P), reveals that transfer RNA recognition by PRORP is similar to that by ribonucleoprotein RNase P.

    • Anthony Gobert
    • , Franziska Pinker
    •  & Philippe Giegé

  • Article
    | Open Access

    How the genome is physically organized is less understood in archaea than in eubacteria or eukaryotes. Laurens et al. measure DNA binding by the Sulfolobus solfataricusproteins Alba1 and Alba2 using single-molecule techniques and conclude that the presence of Alba2 leads to more bridging between DNA.

    • Niels Laurens
    • , Rosalie P.C. Driessen
    •  & Gijs J.L. Wuite

  • Article |

    Polycystic kidney disease family proteins form heteromeric complexes with transient receptor potential channel subunits of the TRPP subfamily. Yu and colleagues find that the polycystic kidney disease protein, PKD1L3, is an ion channel pore-forming subunit in the acid-sensing PKD1L3/TRPP3 complex.

    • Yong Yu
    • , Maximilian H. Ulbrich
    •  & Jian Yang

  • Article |

    The plasma membrane is thought to comprise a patchwork of ordered and disordered microdomains; however, direct evidence for this in intact cells remains elusive. Using unmixing of fluorescence lifetime decays, Owen et al. show that ordered domains occupy a majority of the plasma membrane surface in living cells.

    • Dylan M. Owen
    • , David J. Williamson
    •  & Katharina Gaus

  • Article |

    Rapid synaptic transmission requires efficient recycling of synaptic vesicle membrane proteins. Sochackiet al.use live cell, electron and super-resolution microscopy to visualize exocytosis of vesicular transporters and their rapid recapture in clathrin-rich microdomains in the plasma membrane.

    • Kem A. Sochacki
    • , Ben T. Larson
    •  & Justin W. Taraska

  • Article |

    Spider webs consist of scaffolding silk, which supports the cobweb, and gumfoot silk, which can detach easily from the web upon contact with prey. Here, these different mechanical demands are shown to be met by silk attachments of two distinct architectures using the same pyriform silk secretions.

    • Vasav Sahni
    • , Jared Harris
    •  & Ali Dhinojwala

  • Article
    | Open Access

    Sodium-gated ion channels open and close in response to the flow of ions. Here, McCusker et al.report the open structure of a sodium-gated ion channel pore from a bacterial homologue, and show, by comparison with the closed structure, that the movement of a C-terminal helix is sufficient to open the channel.

    • Emily C. McCusker
    • , Claire Bagnéris
    •  & B.A. Wallace

  • Article |

    In the inner ear, sound waves produce movements in hair cell sterocilia, triggering the opening of ion channels. Hakizimana and colleagues show that the resultant currents change the length of sterocilia, and that these length changes alter the efficiency by which sound is converted into electrical signals.

    • Pierre Hakizimana
    • , William E. Brownell
    •  & Anders Fridberger

  • Article
    | Open Access

    Many drugs exist that target the β-adrenergic receptor, but they have different efficacies. Kofukuet al. use NMR to show that methionine 82 in the transmembrane domain undergoes conformational changes depending on whether agonists or inverse agonists are bound, explaining the differential drug efficacy.

    • Yutaka Kofuku
    • , Takumi Ueda
    •  & Ichio Shimada

  • Article |

    Vesicle trafficking in the cell is likely to involve a tug-of-war between motor proteins of opposing directionality. Guet al. use high-speed single-particle tracking in neurons to uncover rotation of paused cargo vesicles, providing insight into the changing forces as the vesicles change direction.

    • Yan Gu
    • , Wei Sun
    •  & Ning Fang

  • Article |

    Supramolecular interactions allow some small molecules to self-assemble into nanofibres and hydrogels in aqueous environments. Gaoet al.report a hydrogelator that forms fluorescent nanofibres within cells, leading to the visualization of their self-assembly at the endoplasmic reticulum.

    • Yuan Gao
    • , Junfeng Shi
    •  & Bing Xu

  • Article |

    The mitochondrial transcription factor A (TFAM) mediates both mitochondrial transcription and DNA compaction, but how it achieves these two functions is unknown. In this study, TFAM is shown to slide along DNA and cause local melting, suggesting a mechanism for how TFAM modulates both transcription and compaction.

    • Géraldine Farge
    • , Niels Laurens
    •  & Gijs J.L. Wuite

  • Article
    | Open Access

    Flavodoxin requires tight binding of its FMN cofactor to be active, but the residues involved are unknown. In this biophysical study, FMN binding is shown to change from nanomolar to picomolar affinity on extremely slow protein relaxation and the residues responsible for cofactor binding are identified.

    • Yves J.M. Bollen
    • , Adrie H. Westphal
    •  & Carlo P.M. van Mierlo

  • Article |

    Glycoprotein hormone receptors show negative cooperativity following a single molecule of agonist binding to each receptor dimer. Here, constitutively active receptors are shown to display less cooperative allosteric regulation, suggesting a direct relationship between conformational changes in the transmembrane domain and allosteric behaviour of the receptor dimers.

    • Maxime Zoenen
    • , Eneko Urizar
    •  & Sabine Costagliola

  • Article |

    The TREX complex and Nxf1 are involved in the export of mRNA from the nucleus but the precise molecular function of TREX is unclear. Here, the TREX components Aly and Thoc5 are shown to bind to Nxf1 resulting in a change in Nxf1 conformation that permits binding to mRNA and nuclear export.

    • Nicolas Viphakone
    • , Guillaume M. Hautbergue
    •  & Stuart A. Wilson

  • Article |

    Resilin is a polymeric elastic protein that is important for the flight and jumping of insects. Here, the structure-function relationships ofDrosophilaresilin are investigated, and a mechanical model is proposed to account for its elasticity.

    • Guokui Qin
    • , Xiao Hu
    •  & David L. Kaplan

  • Article |

    The bacterial channel protein MscL opens in response to mechanical forces and could be exploited for vesicular-based drug delivery. Doerneret al. show that functional MscL can be expressed in mammalian cells and facilitate the controlled cellular uptake of relatively large, membrane-impermeable bioactive molecules.

    • Julia F. Doerner
    • , Sebastien Febvay
    •  & David E. Clapham

  • Article
    | Open Access

    Following retinalcis/trans isomerisation, the active form of the G-protein-coupled receptor rhodopsin decays to opsin and all-trans-retinal. In this study, arrestin, a regulator of G-protein-coupled receptor activity, is shown to facilitate the concurrent sequestering of toxic all-trans-retinal and regeneration of 11-cis-retinal within the opsin population.

    • Martha E. Sommer
    • , Klaus Peter Hofmann
    •  & Martin Heck

  • Article |

    Cyclic nucleotide-gated channels are apparently voltage insensitive despite having the S4-type voltage sensor. Marchesiet al.show that the gating of wild-type CNGA1 and native CNG channels is voltage-independent in the presence of Li+, Na+ and K+, but that it is voltage-dependent in the presence of Rb+, Cs+ and organic cations.

    • Arin Marchesi
    • , Monica Mazzolini
    •  & Vincent Torre

  • Article
    | Open Access

    The motor protein myosin-V transports cargo along actin filaments, but the biophysical mechanisms by which myosin-V generates force are unclear. Here, optical tweezers and a DNA handle are used to study the forces generated by myosin-V: the mechanism of force generation is found to depend on the load applied.

    • Keisuke Fujita
    • , Mitsuhiro Iwaki
    •  & Toshio Yanagida

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