Biophysics articles within Nature Communications

Featured

  • Article |

    Insertion of proteins into a membrane bilayer driven by the Sec translocon is aided by the attributes of the inserted peptides. Here, Ulmschneider et al.measure the free energies of various insertion events and suggest that the membrane interface plays an important role in translocon-guided TM helix insertion.

    • Martin B. Ulmschneider
    • , Jakob P. Ulmschneider
    •  & Stephen H. White

  • Article |

    The crystal structure of the A2A GPCR suggested that water molecules might form a continuous pathway that becomes disrupted during receptor activation. Here Yuan et al.instead show that a conserved layer of hydrophobic residues forms a gate that opens to form a continuous water channel upon receptor activation.

    • Shuguang Yuan
    • , Slawomir Filipek
    •  & Horst Vogel

  • Article
    | Open Access

    Protein unfolding and translocation through membrane pores occurs in several biological processes and has implications in nanopore technologies. Here, the authors show that the kinetics of unfolding differ depending on which end of the chain enters the pore first.

    • David Rodriguez-Larrea
    •  & Hagan Bayley

  • Article |

    It remains unclear how the dynactin complex activates cytoplasmic dynein motor proteins. Ayloo et al.use single molecule imaging to observe dynein–dynactin behaviour on microtubules, and show that dynactin recruits dynein to microtubules and acts as a brake to slow the motor.

    • Swathi Ayloo
    • , Jacob E. Lazarus
    •  & Erika L. F. Holzbaur

  • Article |

    Heterochromatin is a ‘repressed’ chromatin state involved in the generation of centromeres, the protection of telomeres and the maintenance of genome integrity. Here Swygert et al.show that Sir3 - a key factor in the formation of heterochromatin - promotes a chromatin structure distinct from the canonical 30 nm fibre.

    • Sarah G. Swygert
    • , Benjamin J. Manning
    •  & Craig L. Peterson

  • Article
    | Open Access

    The structural cross-talk between components of the eukaryotic cytoskeleton remains poorly understood. Here the authors engineer an actin-binding microtubule tip-tracking protein that guides microtubule growth along actin bundles, and allows microtubule growing ends to pull and bundle actin filaments.

    • Magdalena Preciado López
    • , Florian Huber
    •  & Marileen Dogterom

  • Article |

    Electrical synaptic transmission is known to be modulated by intracellular magnesium. Here, Palacios-Prado et al.show that electrical synapses formed by connexin36 in the thalamic reticular nucleus are bidirectionally modulated by changes in magnesium concentration via pore-lining sensitive domains.

    • Nicolás Palacios-Prado
    • , Sandrine Chapuis
    •  & Feliksas F. Bukauskas

  • Article
    | Open Access

    Complex molecular interactions occur in the active zone cytomatrix (CAZ) within the presynaptic terminal to regulate synaptic plasticity. Here, the authors use imaging techniques to show that the CAZ is composed of units containing on average 137 Bruchpilot proteins, many of which are arranged into clusters.

    • Nadine Ehmann
    • , Sebastian van de Linde
    •  & Robert J. Kittel

  • Article |

    Unlike most processive motor proteins, the stepping motion of cytoplasmic dynein’s two linked motor domains is not precisely coordinated. Cleary et al.show that the ATPase activity of just one head is required for processive movement, and that tension on the linker gates the release of the motor from microtubules.

    • Frank B. Cleary
    • , Mark A. Dewitt
    •  & Ahmet Yildiz

  • Article |

    Some biological reactions can require thermodynamically unfavourable electron transfer processes, the occurrence of which are not yet fully understood. Here, the authors provide the structural basis of energy transduction during the reductive activation of B12-dependent methyltransferases.

    • Sandra E. Hennig
    • , Sebastian Goetzl
    •  & Holger Dobbek

  • Article |

    At cell–cell adhesions, α-catenin contains a cryptic vinculin-binding site. Here, Yao et al. demonstrate, using magnetic tweezers, that physiologically relevant forces unfurl α-catenin to reveal the vinculin-binding site, and allow the reversible binding of vinculin to mechanically reinforce the adhesion.

    • Mingxi Yao
    • , Wu Qiu
    •  & Jie Yan

  • Article |

    Some viruses possess ‘decoration’ proteins, such as gpD in lambda phage, that stabilize the viral particles in poorly understood ways. Here the authors show that gpD incorporation into lambda particles provides mechanical reinforcement and increased resistance to punctual deformations and collisions.

    • M. Hernando-Pérez
    • , S. Lambert
    •  & P. J. de Pablo

  • Article
    | Open Access

    Although many proteins adopt uneven distributions in the plasma membrane, it is not clear how these nanoscale heterogeneities relate to the general protein patterning of the membrane. Saka et al. use click chemistry to reveal the mesoscale organization of membrane proteins into multi-protein assemblies.

    • Sinem K. Saka
    • , Alf Honigmann
    •  & Silvio O. Rizzoli

  • Article
    | Open Access

    Numerous obstacles posed by cellular subcompartments and structures constrain protein transport in the cell. Here, Baum et al.map the intracellular topology from a diffusing protein’s point of view by measuring the diffusive movements of fluorescently labelled reporter proteins in living cells on multiple time and length scales.

    • Michael Baum
    • , Fabian Erdel
    •  & Karsten Rippe

  • Article |

    Antibody–antigen recognition is one of the important aspects of immunity, but the nanomechanical process of this recognition is not fully understood. Here, using high-speed atomic force microscopy, the authors observe that on membranes containing a high density of immobile antigens antibodies move in a ‘random walking’ motion.

    • Johannes Preiner
    • , Noriyuki Kodera
    •  & Peter Hinterdorfer

  • Article
    | Open Access

    The oxygen-evolving complex of photosystem II converts water into oxygen during photosynthesis, but how this process occurs is not yet fully understood. Here, the authors use modified complexes with reduced reaction rates to study the process of oxygen evolution in more detail.

    • Håkan Nilsson
    • , Fabrice Rappaport
    •  & Johannes Messinger

  • Article
    | Open Access

    Some viruses are spherical particles in which protein components are organized with well-defined icosahedral and local symmetries. Here, Gipson et al. describe a unique arrangement of proteins, breaking all expected local symmetries, in particles of a marine bacterial virus.

    • Preeti Gipson
    • , Matthew L. Baker
    •  & Wah Chiu

  • Article |

    The interaction of water molecules with a protein results in a frictional force that influences protein conformational dynamics and folding, though the nature of the protein also influences the friction. Here, the authors use molecular simulations to examine the origin of this protein contribution.

    • David de Sancho
    • , Anshul Sirur
    •  & Robert B. Best

  • Article
    | Open Access

    Cofactor-mediated energy and electron transfer in photosystem II occurs preferentially through one branch of the reaction centre, despite there being a symmetric path available. Here, the authors use computational methods to determine the influence of protein conformation on this selectivity.

    • Lu Zhang
    • , Daniel-Adriano Silva
    •  & Xuhui Huang

  • Article
    | Open Access

    Novel headphone technology employs bone conduction to enable hearing, but the mechanism behind this remains unclear. Tchumatchenko and Reichenbach now show that bone conduction and subsequent hearing and otoacoustic emissions are in part due to deformation of the cochlear bone.

    • Tatjana Tchumatchenko
    •  & Tobias Reichenbach

  • Article |

    Ribosome-associated protein biogenesis factors act during protein synthesis to facilitate modification, targeting and folding of the nascent polypeptide. Here, Bornemann et al.establish the dynamic interplay between these factors, thus providing new insight into the early steps of protein biogenesis.

    • Thomas Bornemann
    • , Wolf Holtkamp
    •  & Wolfgang Wintermeyer

  • Article |

    Nanopores are promising tools for the detection and characterization of biomolecules. Here, the authors combine experiments and simulations to study how the passage of rigid viruses through solid-state nanopores differs from more flexible biomolecules.

    • Angus McMullen
    • , Hendrick W. de Haan
    •  & Derek Stein

  • Article |

    Telomerase reverse transcriptase extends the ends of linear chromosomes with the aid of an integral RNA subunit. Here, Parks and Stone characterize the translocation kinetics of telomerase identifying distinct steps important for the processivity of the enzyme.

    • Joseph W. Parks
    •  & Michael D. Stone

  • Article |

    Two viral proteins form the nuclear egress complex of herpesviruses, which is essential for the exit of nascent viral capsids from the cell nucleus. Here, the authors use synthetic lipid vesicles to show that the complex can mediate membrane budding in the absence of other cellular factors.

    • Janna M. Bigalke
    • , Thomas Heuser
    •  & Ekaterina E. Heldwein

  • Article |

    Functional changes in protein structures are involved in a large number of biochemical processes. Here, the authors perform a simulation study of known protein structures to show how β-sheets possess the ability to facilitate concerted backbone motions.

    • R. Bryn Fenwick
    • , Laura Orellana
    •  & Xavier Salvatella

  • Article |

    The degradation of chitin and cellulose is dependent on the processivity of degrading enzymes. Here, Igarashi et al. use high-speed atomic force microscopy to visualize the movement of two chitinases (ChiA and ChiB) and show them to move in opposite directions, allowing a molecular mechanism to be proposed.

    • Kiyohiko Igarashi
    • , Takayuki Uchihashi
    •  & Masahiro Samejima

  • Article |

    Thyroid hormone synthesis requires import of iodide ions through the Na+/I− symporter, however its affinity for iodide is surprisingly low. Using a statistical thermodynamics approach, Nicola et al. show that sodium ion binding enhances iodide affinity, revealing a mechanism for iodide transport.

    • Juan P. Nicola
    • , Nancy Carrasco
    •  & L. Mario Amzel

  • Article |

    Terahertz-frequency underdamped vibrational modes in proteins are thought to be involved in biochemical processes, but their observation in solution is difficult. Here, the authors use femtosecond optical Kerr-effect spectroscopy to experimentally identify these modes during enzyme–ligand binding.

    • David A. Turton
    • , Hans Martin Senn
    •  & Klaas Wynne

  • Article |

    Cadherins are calcium-dependent adhesion molecules that can form catch bonds, characterized by longer lifetimes at higher force. Here, Manibog et al. determine the mechanism of catch bond formation, whereby tension induces hydrogen bond formation between opposing extracellular domains in a calcium-dependent manner.

    • Kristine Manibog
    • , Hui Li
    •  & Sanjeevi Sivasankar

  • Article |

    Cells sense their physical environment and reorient in response to cyclic mechanical deformation. Here the authors show that existing models do not adequately explain this phenomenon, and develop a new theory based on the active relaxation of passively stored elastic energy.

    • Ariel Livne
    • , Eran Bouchbinder
    •  & Benjamin Geiger

  • Article |

    In bacteria, chromosomal architecture exhibits spatial and temporal fluctuations, which affect cellular functions. Here, Javer et al. use high-resolution tracking of chromosomal loci in E. colito uncover rare events of unusually large and fast movements, providing new insight into bacterial chromosome dynamics.

    • Avelino Javer
    • , Nathan J. Kuwada
    •  & Marco Cosentino Lagomarsino

  • Article |

    α-synuclein is a protein whose aberrant aggregation is associated with Parkinson’s disease. Here, Fusco et al.characterize α-synuclein bound to lipid membranes using a combination of solution and solid-state NMR spectroscopy and provide insights into the molecular processes associated with the aggregation of this protein.

    • Giuliana Fusco
    • , Alfonso De Simone
    •  & Gianluigi Veglia

  • Article
    | Open Access

    NAD and NADP play fundamentally different roles in cellular metabolism, and yet these pyridine nucleotides cannot be distinguished spectroscopically in living cells. Blacker et al.demonstrate that fluorescence lifetime imaging can be used to quantify NADPH/NADH balance in cultured cells and in the mammalian cochlea.

    • Thomas S. Blacker
    • , Zoe F. Mann
    •  & Michael R. Duchen

  • Article
    | Open Access

    Cell–cell fusion in Caenorhabditis elegans is mediated by EFF-1 and AFF-1 proteins. Here, the authors present an electron cryomicroscopy 3D reconstruction of EFF-1 in the membrane, and combine snapshots of membrane fusion in vitrowith a recently reported crystal structure to propose a mechanism for the fusion process.

    • Tzviya Zeev-Ben-Mordehai
    • , Daven Vasishtan
    •  & Kay Grünewald

Browse broader subjects

Browse narrower subjects

Browse Biophysics across other nature.com journals