Molecular biophysics articles within Nature Communications

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  • Article |

    Binding of the Tudor domain of the PHD finger protein PHF1 to H3K36me3 inhibits Polycomb PRC2 complex methyltransferase activity. Here, Musselman et al.characterize this interaction in the context of the full nucleosome and show dual binding of the PHF1 Tudor domain to H3K36me3 and double-stranded DNA.

    • Catherine A. Musselman
    • , Matthew D. Gibson
    •  & Tatiana G. Kutateladze

  • Article
    | Open Access

    Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.

    • Linda C. Johansson
    • , David Arnlund
    •  & Richard Neutze

  • Article |

    ϕ analysis provides a means to tease apart the dynamics of fast conformational changes in proteins by analysing the thermodynamic impact of point mutations. Purohit et al.apply this approach on a grand scale to map energy changes associated with the opening and closing of an acetylcholine receptor.

    • Prasad Purohit
    • , Shaweta Gupta
    •  & Anthony Auerbach

  • Article |

    Bacterial chemoreceptors regulate the kinase CheA via ligand-induced conformational changes. Using long molecular dynamics simulations, Ortega et al.show that these changes are associated with flipping of the stacked aromatic rings of highly conserved phenylalanine residues within the kinase-activating domain.

    • Davi R. Ortega
    • , Chen Yang
    •  & Igor B. Zhulin

  • Article
    | Open Access

    Helicobacter pylori survives in the acidic environment of the stomach by taking up urea and converting it to ammonia and carbon dioxide, which buffer the bacterial periplasm. Using molecular dynamics simulations, McNulty et al. provide insight into the mechanism of urea uptake through the H. pyloriurea transporter.

    • Reginald McNulty
    • , Jakob P. Ulmschneider
    •  & Martin B. Ulmschneider

  • Article |

    Nck1/2 adaptor proteins control the assembly and activity of protein complexes that promote actin polymerization. Buvall et al.show that Nck1 abundance is regulated by the E3 ubiquitin ligase c-Cbl, which competes for Nck binding with the actin-binding protein synaptopodin in podocytes.

    • Lisa Buvall
    • , Priyanka Rashmi
    •  & Peter Mundel

  • Article
    | Open Access

    Cyclic nucleotide-gated channels mediate olfactory and visual responses. Using a fluorescent cGMP derivative, Nache et al.show that the rate of cyclic nucleotide release from CNGA2 depends on the extent to which this tetrameric receptor is liganded, revealing hysteresis in the gating mechanism.

    • Vasilica Nache
    • , Thomas Eick
    •  & Klaus Benndorf

  • Article |

    Microbial community function depends on metabolic interdependencies between individual species, some of which include electron transfer. Nagarajan et al. use genomic, transcriptomic and modelling approaches to describe the mechanisms supporting the syntrophic relationship between Geobacter metallireducens and Geobacter sulfurreducens.

    • Harish Nagarajan
    • , Mallory Embree
    •  & Karsten Zengler

  • Article |

    Predicting the dynamics and disorder of a protein is a computationally complex task that, until now, has depended on prior knowledge of protein structure. Cilia et al.develop a tool to rapidly predict protein backbone dynamics based on sequence alone.

    • Elisa Cilia
    • , Rita Pancsa
    •  & Wim F. Vranken

  • Article |

    The preference of potassium channels to bind K+ ions over Na+ ions at equilibrium has been proposed to determine their exclusive K+ conductance. Liu and Lockless show that a related, non-selective cation channel also binds only K+ions at equilibrium, suggesting that this property alone does not determine selectivity.

    • Shian Liu
    •  & Steve W. Lockless

  • Article
    | Open Access

    K+ channels are selective for K+ despite the fact that Na+ can bind and conduct through the selectivity filter. Sauer et al. show that a K+-selective NaK2K channel has two high-affinity K+-binding sites, whereas a non-selective NaK2CNG channel has one, and propose a double-barrier mechanism for ion selectivity.

    • David B. Sauer
    • , Weizhong Zeng
    •  & Youxing Jiang

  • Article |

    Regulator of K+ conductance (RCK) domains control the gating of potassium channels in response to ligands such as calcium. Smith et al. solve structures of the MthK RCK domain with varying numbers of calcium ions bound, and reveal the structural basis of allosteric coupling between calcium binding sites.

    • Frank J. Smith
    • , Victor P.T. Pau
    •  & Brad S. Rothberg

  • Article |

    Histone H2A-H2B heterodimers are lost from nucleosomes during transcription by RNA polymerase II. Here Sheinin et al. investigate the behaviour of single nucleosomes subjected to DNA supercoiling and observe a loss of these heterodimers under positive supercoiling, which might have implications for histone turnover during transcription in vivo.

    • Maxim Y. Sheinin
    • , Ming Li
    •  & Michelle D. Wang

  • Article
    | Open Access

    α-synuclein is implicated in neurodegenerative diseases. Bousset et al. generate two α-synuclein polymorphs and find differences in aggregation, function and toxicity, suggesting that these altered properties may be the cause for differences in disease progression.

    • Luc Bousset
    • , Laura Pieri
    •  & Ronald Melki

  • Article |

    The ClC family of chloride channels are homodimeric and contain two pores that are gated simultaneously. Bennetts and Parker combine homology modelling and mutant-cycle analysis to reveal structural linkages important for coordination of gating between subunits.

    • Brett Bennetts
    •  & Michael W. Parker

  • 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 |

    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
    | 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 |

    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
    | 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

    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 |

    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 |

    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 |

    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 |

    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
    | 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

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