Biophysics articles within Nature Communications

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  • Article
    | Open Access

    Prokaryotic voltage-gated sodium channels possess dynamically disordered cytoplasmic C-terminal domains. Bagnéris et al. present the structure of the Magnetococcus marinusNavMs pore and C-terminal domain and reveal its role in coupling channel inactivation and opening.

    • Claire Bagnéris
    • , Paul G. DeCaen
    •  & B. A. Wallace

  • Article
    | Open Access

    Transport of DNA molecules across lipid membranes requires protein conduits such as the nuclear pore complex. Franceschiniet al.engineer an artificial sequence-selective DNA transporter by attaching gating oligonucleotides to a bacterial nanopore.

    • Lorenzo Franceschini
    • , Misha Soskine
    •  & Giovanni Maglia

  • Article |

    Messenger RNAs and their associated proteins are transported from the nucleus through highly selective nuclear pore complexes. Using ultrahigh resolution single-molecule imaging, the authors visualise the path taken by each messenger RNA as it negotiates the pore’s selectivity filter.

    • Jiong Ma
    • , Zhen Liu
    •  & Weidong Yang

  • Article |

    TMEM16-channel family members have been shown to be involved in Ca2+-dependent lipid scrambling, but whether they have intrinsic scramblase activity remains controversial. Malvezzi et al. identify a TMEM16 family member in Aspergillus in which a single Ca2+-binding site regulates intrinsic channel and scramblase activities.

    • Mattia Malvezzi
    • , Madhavan Chalat
    •  & Alessio Accardi

  • Article |

    Srs2 is a DNA helicase and single-stranded DNA translocase that prevents homologous recombination by dismantling Rad51 filaments. Qiu et al.use single-molecule techniques to describe Rad51 filament formation and show that Srs2 displays repetitive activity on single-stranded DNA, which prevents re-formation of Rad51 filaments after dismantling.

    • Yupeng Qiu
    • , Edwin Antony
    •  & Sua Myong

  • Article |

    Actin normally polymerizes into filaments in a cooperative manner, with nucleation and elongation phases. Skillman et al. show that actin from the protozoan parasite Toxoplasma gondiipolymerizes in an isodesmic manner, without any evidence of nucleation, resulting in filaments that are very short and unstable.

    • Kristen M. Skillman
    • , Christopher I. Ma
    •  & L. David Sibley

  • Article |

    While small molecules that destabilize actin filaments are readily available, artificially stimulating actin polymerization in cells typically involves genetic manipulation. Here, the authors design cell-permeable branched polyamines that promote lamellipodium formation by stimulating actin polymerization.

    • Iliana Nedeva
    • , Girish Koripelly
    •  & Daniel Riveline

  • Article |

    Patchiness in the distribution of phytoplankton promotes many of the ecological interactions that underpin the marine food web. This study shows that turbulence, ubiquitous in the ocean, counter-intuitively ‘unmixes’ a population of motile phytoplankton, generating intense, small-scale patchiness in its distribution.

    • William M. Durham
    • , Eric Climent
    •  & Roman Stocker

  • Article
    | Open Access

    The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint.

    • Johannes Hohlbein
    • , Louise Aigrain
    •  & Achillefs N. Kapanidis

  • Article
    | Open Access

    The thermodynamics of unwinding polynucleotide duplexes can be determined from energy changes for DNA and mRNA interactions. Here the authors show that the ratio between mRNA/DNA and DNA/DNA duplex stability upstream of the 3′- spice sites is a characteristic that can contribute to intron–exon recognition.

    • Marina N. Nedelcheva-Veleva
    • , Mihail Sarov
    •  & Stoyno S. Stoynov

  • Article
    | Open Access

    The switch from linear to cyclic electron flow has long been thought to rely on the migration of antenna proteins from Photosystem II to Photosystem I. Takahashi et al. report that this is not the case and that cyclic electron flow is tuned by the intrachloroplastic redox power.

    • Hiroko Takahashi
    • , Sophie Clowez
    •  & Fabrice Rappaport

  • Article |

    Changes in DNA methylation during mammalian spermatogenesis are poorly understood. The authors show that the content of 5-hydroxymethylcytosine, a stable intermediate of DNA demethylation, changes dynamically during mouse spermatogenesis and is associated with functional genomic regions and transcription.

    • Haiyun Gan
    • , Lu Wen
    •  & Fuchou Tang

  • Article
    | Open Access

    Voltage-gated potassium channels open and close in response to changes in transmembrane potential, but their opening mechanism is poorly understood. Here, free energy molecular dynamics simulations show that strain accumulates as the pore closes, which subsequently drives opening.

    • Philip W. Fowler
    •  & Mark S. P. Sansom

  • Article |

    Dehydrated hereditary stomatocytosis is a genetic condition in which the permeability of red blood cells to cations in increased. Albuisson and colleagues find that mutations in the mechanically-activated PIEZO1 ion channel are the major cause of the disease and result in more slowly inactivating currents.

    • Juliette Albuisson
    • , Swetha E Murthy
    •  & Ardem Patapoutian

  • Article |

    Formins are a family of protein complexes that accelerate actin filament nucleation and elongation. Jegou et al.show that the formin mDia1 can generate mechanical tension in actin filaments, while conversely, pulling forces applied by viscous drag increase formin elongation activity.

    • Antoine Jégou
    • , Marie-France Carlier
    •  & Guillaume Romet-Lemonne

  • Article |

    Live cell imaging have recently revealed that transcription factors spend up to 4 min to find and bind their chromosomal binding site. Grönlund et al. show that this slow search process leads to tradeoffs between strength and speed of negative autoregulation for effective noise suppression.

    • Andreas Grönlund
    • , Per Lötstedt
    •  & Johan Elf

  • Article
    | Open Access

    The division of a single eukaryotic cell into two requires actomyosin-dependent contraction. Here the authors show that lysine methylation of actin inhibits contractility during cytokinesis by blocking its association with myosin, and this modification is reversed at the contractile ring by the demethylase ALKBH4.

    • Ming-Ming Li
    • , Anja Nilsen
    •  & Yun-Gui Yang

  • Article |

    Outer hair cell electromotility contributes to the cochlear amplifier during hearing. Here the authors find that targeted-deletion of the gap junction protein connexin 26 results in reduced electromotility of outer hair cells, reduced cochlear amplification and hearing loss in mice.

    • Yan Zhu
    • , Chun Liang
    •  & Hong-Bo Zhao

  • 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

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