Biophysics articles within Nature


  • News & Views Forum |

    Cutting-edge X-ray sources have enabled the structural dynamics of proteins to be tracked during biochemical processes, but the findings have been questioned. Two experts discuss the implications of a study that digs into this issue.

    • Richard Neutze
    •  & R. J. Dwayne Miller
  • Article
    | Open Access

    Ultrafast time-resolved serial femtosecond crystallography is used to investigate a photodissociation reaction in a protein, revealing the strong impact of the pump laser fluence on the structural changes  and the reaction mechanism.

    • Thomas R. M. Barends
    • , Alexander Gorel
    •  & Ilme Schlichting
  • Research Briefing |

    Rapid communication between intracellular structures such as the endoplasmic reticulum and the mitochondria is crucial for the coordinated functioning of cells. Such interactions occur mainly at sites where the compartments are in direct contact, and are mediated by specific tethering machinery. High-speed single-molecule tracking reveals a well-regulated interface at which many rapid binding and unbinding events provide highly adaptable interactions.

  • Article
    | Open Access

    Serial femtosecond crystallography reveals the structural dynamics of photosystem II during the S-state transitions that produce dioxygen, providing insight into electron transfer, water insertion, proton release and O–O bond formation on sub-microsecond timescales.

    • Hongjie Li
    • , Yoshiki Nakajima
    •  & Jian-Ren Shen
  • Article |

    A computational model generates conformational ensembles of 28,058 intrinsically disordered proteins and regions (IDRs) in the human proteome and sheds light on the relationship between sequence, conformational properties and functions of IDRs.

    • Giulio Tesei
    • , Anna Ida Trolle
    •  & Kresten Lindorff-Larsen
  • Article
    | Open Access

    High-speed molecular tracking is integrated with three-dimensional electron microscopy to map the diffusion distribution and ultrastructure of endoplasmic reticulum-mitochondria contact sites, revealing the ability of high-speed single-molecule imaging to map contact site interface structures and corresponding diffusion landscapes.

    • Christopher J. Obara
    • , Jonathon Nixon-Abell
    •  & Jennifer Lippincott-Schwartz
  • Article
    | Open Access

    Analysis of the effects of more than 26,000 KRAS mutations on abundance and interactions with six other proteins is used to construct an energy landscape of KRAS and identify allosteric drug target sites.

    • Chenchun Weng
    • , Andre J. Faure
    •  & Ben Lehner
  • Article |

    Structures of human vesicular monoamine transporter 2 in complexes with serotonin and three clinical drugs provide insights into the structural basis for serotonin transport and inhibition of transporter activity by the drugs.

    • Di Wu
    • , Qihao Chen
    •  & Daohua Jiang
  • Article |

    As well as being the substrate for the lipopolysaccharide transport protein complex comprising LptA–G, lipopolysaccharide binding to Lpt proteins promotes their assembly into a bridge linking the inner and outer membranes of Gram-negative bacteria.

    • Lisa Törk
    • , Caitlin B. Moffatt
    •  & Daniel Kahne
  • Article |

    The intricate molecular architecture and interactions of the human cardiac myosin filament offer insights into cardiac physiology, disease and drug therapy.

    • Debabrata Dutta
    • , Vu Nguyen
    •  & Roger Craig
  • Article
    | Open Access

    Upon hyperpolarization, the S4 voltage-sensing segment of sea urchin SLC9C1 moves down, removing inhibition caused by an intracellular helix and enabling Na+/H+ exchange, leading to pH-dependent activation of sAC and sperm chemotaxis.

    • Hyunku Yeo
    • , Ved Mehta
    •  & David Drew
  • News & Views |

    Proteins can condense to form membraneless organelles, which act as vessels for biochemical reactions in cells. An investigation shows that protein condensation is also a cellular mechanism for controlling water availability.

    • J. Pedro de Souza
    •  & Howard A. Stone
  • Article
    | Open Access

    Water thermodynamics drive changes in macromolecular assembly that rapidly restore intracellular water availability in response to physiological fluctuations in temperature, pressure and osmotic strength.

    • Joseph L. Watson
    • , Estere Seinkmane
    •  & Emmanuel Derivery
  • Article |

    The first heartbeat of a zebrafish was captured, and development of cardiac excitability and conduction around this singular event were analysed, showing how development of single-cell properties produces a transition from quiescence to coordinated beating.

    • Bill Z. Jia
    • , Yitong Qi
    •  & Adam E. Cohen
  • Article |

    High-speed atomic force microscopy single-molecule imaging and cryo-EM analysis discover and reveal the structure of a TRPV3 pentamer, providing evidence for a non-canonical pentameric TRP-channel assembly, laying the foundation for new directions in TRP channel research.

    • Shifra Lansky
    • , John Michael Betancourt
    •  & Simon Scheuring
  • News & Views |

    It is well established that proteins in the TRP family of ion channels assemble from four subunits. But do they always do this? A five-subunit structure has now been observed, and might be involved in channel regulation.

    • Ute A. Hellmich
  • Research Briefing |

    Protein sequences vary widely in their folding stabilities (the energetic favourability of folded compared with unfolded conformations), and protein alterations that affect stability have profound effects on evolution, health and disease, and biotechnological applications. An innovative method has made it possible to measure these stabilities on a massive scale, revealing evolutionary trends and opening up possibilities for machine learning.

  • Article |

    Two highly charged disordered human proteins phase-separate into viscous complex coacervates while retaining their rapid conformational dynamics through pico- to nanosecond exchange of short-lived side-chain interactions.

    • Nicola Galvanetto
    • , Miloš T. Ivanović
    •  & Benjamin Schuler
  • Article
    | Open Access

    Using a heralded single-photon source along with coincidence counting, we establish time correlation functions for B800 excitation and B850 fluorescence emission and demonstrate that both events involve single photons.

    • Quanwei Li
    • , Kaydren Orcutt
    •  & K. Birgitta Whaley
  • Article |

    A structural and functional analysis of the systems involved in oligosaccharide uptake in gut Bacteroidetes describes multicomponent complexes termed utilisomes that include pre-processing and transport subunits.

    • Joshua B. R. White
    • , Augustinas Silale
    •  & Neil A. Ranson
  • Article
    | Open Access

    The authors introduce a single-molecule DNA-barcoding method, resolution enhancement by sequential imaging, that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents.

    • Susanne C. M. Reinhardt
    • , Luciano A. Masullo
    •  & Ralf Jungmann
  • Article |

    Systematic alteration of HIV-1 TAR RNA and quantitative determination of its propensity to bind to the Tat protein establish a key role role for a rare and short-lived RNA state in Tat-dependent transactivation in cells.

    • Megan L. Ken
    • , Rohit Roy
    •  & Hashim M. Al-Hashimi
  • Article |

    Interactions between the endoplasmic reticulum membrane protein complex (EMC) and the high-voltage-activated calcium channel CaVα2δ are mutually exclusive, and EMC-to-CaVα2δ hand-off involves a divalent ion-dependent step and CaV1.2 element ordering.

    • Zhou Chen
    • , Abhisek Mondal
    •  & Daniel L. Minor Jr
  • Article |

    A study presents evidence to support a model in which liquid–liquid phase separation of components of the transport machinery mediates formation of transient protein transport channels on peroxisomes.

    • Rini Ravindran
    • , Isabel O. L. Bacellar
    •  & Stephen W. Michnick
  • Article |

    After 600 rounds of selection, anaerobic snowflake yeast evolved to be macroscopic, becoming around 20,000 times larger (approximately mm scale) and about 10,000-fold more biophysically tough, while retaining a clonal multicellular life cycle.

    • G. Ozan Bozdag
    • , Seyed Alireza Zamani-Dahaj
    •  & William C. Ratcliff
  • Article
    | Open Access

    Using serial femtosecond X-ray cystallography, we provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, specifically the S3→[S4]→S0 transition where O2 is formed.

    • Asmit Bhowmick
    • , Rana Hussein
    •  & Vittal K. Yachandra
  • Article
    | Open Access

    Microsecond infrared spectroscopy together with quantum chemistry reveal the rate-determining proton and electron movements and identify an oxygen-radical state of the manganese cluster as the S4 state.

    • Paul Greife
    • , Matthias Schönborn
    •  & Holger Dau
  • Article
    | Open Access

    Using single-molecule imaging, the authors show that Smc5/6 forms DNA loops by extrusion, which establishes DNA loop extrusion as a conserved mechanism among eukaryotic SMC complexes.

    • Biswajit Pradhan
    • , Takaharu Kanno
    •  & Eugene Kim
  • Article |

    Cryo-electron microscopy analyses reveal adaptations that facilitate the octopus chemotactile receptor’s evolutionary transition from an ancestral role in neurotransmission to detecting greasy environmental agonists for ‘taste by touch’ sensory behaviour.

    • Corey A. H. Allard
    • , Guipeun Kang
    •  & Nicholas W. Bellono
  • Article |

    Octopus and squid use cephalopod-specific chemotactile receptors to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles.

    • Guipeun Kang
    • , Corey A. H. Allard
    •  & Ryan E. Hibbs
  • Article
    | Open Access

    A structure–function analysis of cystic fibrosis transmembrane conductance regulator shows its two nucleotide-binding domains dimerize before channel opening, and reveals a mechanism through which conformational changes in the channel regulate chloride conductance.

    • Jesper Levring
    • , Daniel S. Terry
    •  & Jue Chen
  • Article |

    By using in vivo ultrafast TA spectroscopy, extraction of electrons directly from photoexcited PSI and PSII in cyanobacterial cells using exogenous electron mediators is demonstrated.

    • Tomi K. Baikie
    • , Laura T. Wey
    •  & Jenny Z. Zhang
  • Research Briefing |

    Our sense of smell enables us to perceive a universe of odours. Cryo-electron microscopy has provided an atomic-resolution picture of how an odour molecule is recognized by one of the hundreds of odorant receptors encoded in the human genome, providing a first view into the chemical logic of olfaction.

  • Article |

    Through the use of cryo-electron microscopy and molecular dynamics stimulations, mechanistic insight into the binding of an odorant to the human odorant receptor OR51E2 is provided.

    • Christian B. Billesbølle
    • , Claire A. de March
    •  & Aashish Manglik