Biophysics

  • Article
    | Open Access

    Cytoskeletal networks support and direct cell shape and guide intercellular transport, but relatively little is understood about the self-organization of cytoskeletal components on the scale of an entire cell. Here, authors use an in vitro system and observe the assembly of different types of actin networks and the condensation of membrane-bound actin into single rings.

    • Thomas Litschel
    • , Charlotte F. Kelley
    •  & Petra Schwille
  • Article
    | Open Access

    P450 oxidoreductase (POR) selectively activates numerous cytochromes P450 (CYP), crucial for metabolism of drugs, steroids and xenobiotics and natural product biosynthesis. Here, the authors identify ligands that bind POR and bias its specificity towards CYP redox partners, activating distinct metabolic cascades in cells.

    • Simon Bo Jensen
    • , Sara Thodberg
    •  & Nikos S. Hatzakis
  • Article
    | Open Access

    The intrinsically disordered acidic activation domain (AD) of the yeast transcription factor Gal4 acts through binding to the Med15 subunit of the Mediator complex. Here, the authors show that Gal4 interacts with Med15 through an identical fuzzy binding mechanism as Gcn4 AD, which has a different sequence, revealing a common sequence-independent mechanism for AD-Mediator binding. In contrast, Gal4 AD binds to the Gal80 repressor as a structured polypeptide, which strongly suggests that the structured binding partner dictates the type of protein–protein interaction for an intrinsically disordered protein.

    • Lisa M. Tuttle
    • , Derek Pacheco
    •  & Rachel E. Klevit
  • Article
    | Open Access

    Quantifying rapid and small cellular forces is a major challenge in mechanobiology. Here, the authors show a >2-fold spatially and >10-fold temporally force sampling improvement combining traction force microscopy with total internal reflection fluorescence super-resolution structured illumination microscopy.

    • Liliana Barbieri
    • , Huw Colin-York
    •  & Marco Fritzsche
  • Article
    | Open Access

    Dynamic cell wall assembly is key to cell shape maintenance during bacterial growth. Here, the authors present a method that allows high-resolution analysis of active and inert zones of cell wall growth during bacterial elongation. They also formulate a mathematical model to predict the partitioning of cell wall-anchored proteins following cell division.

    • Yi-Jen Sun
    • , Fan Bai
    •  & Chien-Jung Lo
  • Article
    | Open Access

    Structural and functional characterization of the full-length TRPV1 channel from the thirteen-lined ground squirrel reveal the architecture of the extracellular cap domain and the intracellular C-terminus, and suggest a role of the cap domain in TRPV1 conductance and ion selectivity.

    • Kirill D. Nadezhdin
    • , Arthur Neuberger
    •  & Alexander I. Sobolevsky
  • Article
    | Open Access

    Reovirus endocytosis depends on junctional adhesion molecule A (JAM-A) and β1 integrin binding. Here, Koehler et al. use single-virus force spectroscopy and confocal microscopy to demonstrate a direct interaction between reovirus and β1 integrins via viral capsid protein λ2, which promotes clathrin recruitment to cell-bound reovirus.

    • Melanie Koehler
    • , Simon J. L. Petitjean
    •  & David Alsteens
  • Article
    | Open Access

    Quantifying rapidly progressing three-dimensional forces generated by cells remains a major challenge in mechanobiology. Here, the authors show that combining traction force microscopy with astigmatic imaging permits sensitive out-of-plane force estimation on the second timescale.

    • Di Li
    • , Huw Colin-York
    •  & Marco Fritzsche
  • Article
    | Open Access

    Intrinsically disordered FG-Nups line the Nuclear Pore Complex (NPC) lumen and form a selective barrier where transport of most proteins is inhibited, whereas specific transporter proteins are able to pass. Here, the authors reconstitute the selective behaviour of the NPC by introducing a rationally designed artificial FG-Nup that demonstrates that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.

    • Alessio Fragasso
    • , Hendrik W. de Vries
    •  & Cees Dekker
  • Article
    | Open Access

    The order and variability of bacterial chromosome organization, contained within the distribution of chromosome conformations, are unclear. Here, the authors develop a fully data-driven maximum entropy approach to extract single-cell 3D chromosome conformations from Hi-C experiments on the model organism Caulobacter crescentus.

    • Joris J. B. Messelink
    • , Muriel C. F. van Teeseling
    •  & Chase P. Broedersz
  • Article
    | Open Access

    Fick’s laws describe the essential physics of diffusion, but it is challenging to extend them to systems out of equilibrium. The authors derive the diffusivity of particles near active carpets - a surface covered with hydrodynamic actuators, which provides a framework for transport in living matter.

    • Francisca Guzmán-Lastra
    • , Hartmut Löwen
    •  & Arnold J. T. M. Mathijssen
  • Article
    | Open Access

    Eukaryotic DNA replication is regulated to ensure copying of the genome (only) once per cell cycle. Here the authors, using optical trapping and confocal microscopy, demonstrate the dynamics of the origin recognition complex and subsequent intermediates that lead up to the loading of an MCM helicase onto DNA.

    • Humberto Sánchez
    • , Kaley McCluskey
    •  & Nynke H. Dekker
  • Article
    | Open Access

    Plasmodium falciparum moves by an atypical process called gliding motility which comprises of atypical myosin A (PfMyoA) and filaments of the dynamic and divergent PfActin-1 (PfAct1). Here authors present the cryo-EM structure of PfMyoA bound to filamentous PfAct1 stabilized with jasplakinolide and provide insights into the interactions that are required for the parasite to produce the force and motion required for infectivity.

    • Julien Robert-Paganin
    • , Xiao-Ping Xu
    •  & Dorit Hanein
  • Article
    | Open Access

    The nuclear lamina bridges mechanical forces from the cytoskeleton to the nucleus, and while Lamin A/C is known to be crucial for this process, its regulation remains unclear. Here the authors show that levels of Lamin A/C scale with apico-basal compression of cells independently of tissue stiffness using Drosophila epithelial tissues and mammalian cells.

    • K. Venkatesan Iyer
    • , Anna Taubenberger
    •  & Frank Jülicher
  • Article
    | Open Access

    TEM-1 β-lactamase evolved from ancestral enzymes that degraded a variety of β-lactam antibiotics with moderate efficiency and degrades β-lactam antibiotics with a strong preference for penicillins. Here authors developed a computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism and show a putative Precambrian β-lactamase that mimics the modern TEM-1 β-lactamase with only 21 amino acid replacements.

    • Tushar Modi
    • , Valeria A. Risso
    •  & S. Banu Ozkan
  • Article
    | Open Access

    Buried charged networks in proteins are often important for their biological functionality and are believed to destabilise the protein fold. Here, the authors combine computational design, MD simulations, biophysical experiments, NMR and X-ray crystallography to design and characterise artificial 4α-helical proteins with buried charged elements. They analyse their conformational landscapes and observe that the ion-pairs are stabilised by amphiphilic residues that electrostatically shield the charged motif, which increases structural stability.

    • Mona Baumgart
    • , Michael Röpke
    •  & Ville R. I. Kaila
  • Article
    | Open Access

    Here, the authors present DisCo (Disassembly of Condensates), a method that allows the fast, inducible, and specific disruption of tagged condensates in mammalian cells. DisCo uses chemical dimerizers to induce the recruitment of a ligand into condensates leading to condensate disassembly.

    • Carmen N. Hernández-Candia
    • , Sarah Pearce
    •  & Chandra L. Tucker
  • Article
    | Open Access

    Chromosome segregation requires the association of the kinetochore protein complex with a specialized nucleosome at the centromere. Here, the authors present cryo-EM and mutational studies that provide insights into the structure of the budding yeast centromeric nucleosome and how the centromere CBF3 protein complex guides its formation.

    • Ruifang Guan
    • , Tengfei Lian
    •  & Yawen Bai
  • Article
    | Open Access

    Super-resolution microscopy and single molecule fluorescence spectroscopy require optimisation of the temporal or spatial resolution, which are usually mutually exclusive. Here the authors report a GPU-supported, camera-based strategy to achieve high spatial and temporal resolution from the same dataset.

    • Jagadish Sankaran
    • , Harikrushnan Balasubramanian
    •  & Thorsten Wohland
  • Article
    | Open Access

    Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.

    • Saminathan Ramakrishnan
    • , Jason R. Stagno
    •  & Yun-Xing Wang
  • Article
    | Open Access

    Sensory perception and metabolic homeostasis are known to deteriorate with ageing, while mechanisms underlying their deterioration remain poorly understood. Here, the authors demonstrate that decrease of intraflagellar transport in the cilia of sensory neurons impairs sensory perception and metabolism in ageing C. elegans.

    • Yincong Zhang
    • , Xiaona Zhang
    •  & Yidong Shen
  • Article
    | Open Access

    Bio-mimetic motion has been hard to achieve due to a lack of biocompatible conditions. Here, the authors report the creation of a liposome-stabilised aqueous PEG/dextran Pickering-like emulsion system with motion induced by the Marangoni effect and characterised by negative chemotaxis.

    • Shaobin Zhang
    • , Claudia Contini
    •  & Oscar Ces
  • Article
    | Open Access

    X-ray fee-electron lasers (XFELs) enable time-resolved crystallography experiments and the structure determination of proteins with little or no radiation damage. However currently it is unknown whether the designated 4.5 MHz maximum pulse rate for the European XFEL could lead to sample damage caused by shock waves from preceding pulses. Here, the authors address this question by performing a X-ray pump X-ray probe experiment on haemoglobin microcrystals at the Stanford XFEL facility that mimics the 4.5 MHz data collection mode and observe structural changes and a drop in diffraction data quality of the crystals.

    • Marie Luise Grünbein
    • , Alexander Gorel
    •  & Ilme Schlichting
  • Article
    | Open Access

    Adeno-associated viruses (AAVs) have emerged as promising gene therapy vectors.The AAV capsid consists of 60 subunits made up from three distinct viral proteins (VPs). Here authors record high-resolution native mass spectra of intact AAV capsids to assess the VP stoichiometries in a panel of serotypes and reveals an extremely heterogeneous population of capsids of variable composition.

    • Tobias P. Wörner
    • , Antonette Bennett
    •  & Albert J. R. Heck
  • Article
    | Open Access

    The authors generated a Synthetic Morphogenic Membrane System by encapsulating a dynamic microtubule aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. This reconstitution of artificial proto-cells reveals how non-equilibrium phenomena affect cellular information processing in morphogenesis.

    • Konstantin Gavriljuk
    • , Bruno Scocozza
    •  & Philippe I. H. Bastiaens
  • Article
    | Open Access

    FUS/EWS/TAF15 (FET) fusion oncoproteins contain low complexity domain which forms biomolecular condensates that recruit RNA polymerase II. Here the authors develop a single-molecule assay to visualize this phenomenon providing in vitro evidence to support causative relationship between the formation of condensates on DNA and gene transcription. Furthermore, they also determine a threshold number of fusion-binding DNA satellite elements required for the formation of FET protein condensates.

    • Linyu Zuo
    • , Guanwei Zhang
    •  & Zhi Qi
  • Article
    | Open Access

    The lipid regulation of mammalian ion channel function has emerged as a fundamental mechanism in the control of electrical signalling and transport specificity. Here, the authors combine molecular dynamics simulations, mutagenesis, and electrophysiology to provide mechanistic insights into how lipophilic molecules alter gating kinetics and K+ currents of hERG1.

    • Williams E. Miranda
    • , Jiqing Guo
    •  & Sergei Yu. Noskov
  • Article
    | Open Access

    Realizing wearable sensors for blood pressure (BP) monitoring with clinically-acceptable performance remains a significant challenge. Here, the authors report a continuous noninvasive blood pressure measurement system featuring a volume control technique for small wearable sensors.

    • Jürgen Fortin
    • , Dorothea E. Rogge
    •  & Bernd Saugel
  • Article
    | Open Access

    An EGFR mutant with kinase domain duplication (EGFR-KDD) was previously identified in an index patient, but the functional and therapeutic implications remain unclear. Here, the authors show that KDD occurs in other ErbB receptors in multiple cancers, and characterize the mechanism and inhibition of EGFR-KDD.

    • Zhenfang Du
    • , Benjamin P. Brown
    •  & Christine M. Lovly
  • Article
    | Open Access

    How euchromatin organisation and transcription are related is unclear. Here, the authors observe the dynamics of euchromatin organization showing that accumulating RNA recruits RNA-binding proteins that together with transcribed euchromatin separate from non-transcribed euchromatin, forming microphases.

    • Lennart Hilbert
    • , Yuko Sato
    •  & Nadine L. Vastenhouw
  • Article
    | Open Access

    It is currently challenging to identify protein structures at low concentrations. Here the authors report optical tweezers-coupled Raman spectroscopy to generate tunable and reproducible SERS enhancements with single-molecule level sensitivity and use the method to detect protein structural features.

    • Xin Dai
    • , Wenhao Fu
    •  & Jinqing Huang
  • Article
    | Open Access

    Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, which form condensates at low salt concentrations, can reenter a phase-separated regime at high salt concentrations.

    • Georg Krainer
    • , Timothy J. Welsh
    •  & Tuomas P. J. Knowles
  • Article
    | Open Access

    The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.

    • Tomoaki Kawakami
    • , Long-Jiang Yu
    •  & Zheng-Yu Wang-Otomo
  • Article
    | Open Access

    In cells, DNA is arranged into topologically-constrained (supercoiled) structures, but how this supercoiling affects the detailed double-helical structure of DNA remains unclear. Here authors use atomic force microscopy and atomistic molecular dynamics simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution.

    • Alice L. B. Pyne
    • , Agnes Noy
    •  & Sarah A. Harris
  • Article
    | Open Access

    Pentameric ligand-gated ion channels (pLGICs) are key players in neurotransmission and have been shown to be modulated by the lipid environment, however the underlying mechanism is not well understood. Here, the authors report structures of the pLGIC 5-HT3A serotonin receptor reconstituted into lipid bilayer discs and reveal lipid–protein interactions as well as asymmetric activation of the homopentameric receptor.

    • Yingyi Zhang
    • , Patricia M. Dijkman
    •  & Mikhail Kudryashev
  • Article
    | Open Access

    Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.

    • Clarisse Uwizeye
    • , Johan Decelle
    •  & Giovanni Finazzi
  • Article
    | Open Access

    Structures of mu-opioid receptor (mOR) in complex with morphine derivatives have been determined; but the structural basis of mOR activation by fentanyl-like synthetic opioids remains unclear. Here, authors use state-of-the-art simulation techniques and discover a secondary binding mode which is only accessible when the conserved His297 adopts a neutral HID tautomer state.

    • Quynh N. Vo
    • , Paween Mahinthichaichan
    •  & Christopher R. Ellis
  • Article
    | Open Access

    Epigallocatechin gallate (EGCG) is a catechin flavonoid which induces apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Here authors use an interdisciplinary approach to show a direct interaction between EGCG and the tumor suppressor p53 and demonstrate that EGCG inhibits ubiquitination of p53 by MDM2.

    • Jing Zhao
    • , Alan Blayney
    •  & Chunyu Wang
  • Article
    | Open Access

    Mapping free energy landscapes of complex multi-funneled metamorphic proteins and weakly-funneled intrinsically disordered proteins (IDPs) remains challenging. Here authors present a parallel-tempering method that takes advantage of accelerated water dynamics for efficient and accurate conformational sampling across a wide variety of proteins.

    • Rajeswari Appadurai
    • , Jayashree Nagesh
    •  & Anand Srivastava
  • Article
    | Open Access

    Endocannabinoids are ligands of cannabinoid receptors and a promising target for pain management. Here, the authors report a class of lipids formed by the epoxidation of N-arachidonoyl dopamine and N-arachidonoyl serotonin by cytochrome P450 epoxygenases, which reciprocally regulate canabinoid receptors and display anti-inflammatory activity.

    • William R. Arnold
    • , Lauren N. Carnevale
    •  & Aditi Das
  • Article
    | Open Access

    Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. Here authors investigate the assembly of two computationally designed, 120-subunit icosahedral complexes and find that assembly of each material from its two constituent protein building blocks was highly cooperative.

    • Adam J. Wargacki
    • , Tobias P. Wörner
    •  & Neil P. King
  • Article
    | Open Access

    The conversion of auditory and vestibular stimuli into electrical signals is initiated by force transmitted to a mechanotransduction channel through the tip link. Here authors show that a single tip-link bond is more mechanically stable relative to classic cadherins, and that the double stranded tip-link connection is stabilized by single strand rebinding facilitated by strong cis-dimerization domains.

    • Eric M. Mulhall
    • , Andrew Ward
    •  & Wesley P. Wong