Biophysics articles within Nature Communications

Featured

  • Article
    | Open Access

    Cells exhibit exceptional chemical sensitivity, yet we haven’t fully understood how they achieve it. Here the authors consider the mutual information between signals and two coupled sensors as a proxy for sensing performance and show its optimisation depending on noise level and signal statistics.

    • Vudtiwat Ngampruetikorn
    • , David J. Schwab
    •  & Greg J. Stephens

  • Article
    | Open Access

    Assembling synthetic plant cell is difficult due to the presence of primary cell wall. Here, the authors describe the assembly of lipid-containing bodies that can be coated with cellulose and pectin, and show how these so-called plantosomes can be manipulated by changing surrounding milieu.

    • T. Paulraj
    • , S. Wennmalm
    •  & A. J. Svagan

  • Article
    | Open Access

    Although the permeation mechanisms for K+ and Na+ channels have been extensively studied, the ion permeation mechanism through Ca2+ channels was largely unknown. Here the authors develop a multisite Ca2+ model that can be used in the framework of classical MD simulations to study Ca2+ in a quantitative manner, and use it to investigate the ion permeation mechanism of the ryanodine receptor 1.

    • Aihua Zhang
    • , Hua Yu
    •  & Chen Song

  • Article
    | Open Access

    The organisation of plasma membrane receptors is important for their function. Here the authors combine lattice light-sheet microscopy with 3D single-molecule localisation microscopy (dSTORM) and single-particle tracking to study the distribution and motility of several surface receptors.

    • Felix Wäldchen
    • , Jan Schlegel
    •  & Markus Sauer

  • Article
    | Open Access

    The mussel byssus cuticle is a wear-resistant and extensible metalloprotein composite. Here, the authors probed the cuticle nanostructure and composition before, during and after fabrication revealing a crucial role of metal-binding proteins that self-organize via liquid-liquid phase separation.

    • Franziska Jehle
    • , Elena Macías-Sánchez
    •  & Matthew J. Harrington

  • Article
    | Open Access

    The O-antigen of LPS is known to limit the binding of antibody to bacterial surface antigens. Here the AUs show that the chemical and physical structure of the O-antigen are central factors in limiting the exposure of surface antigens to antibodies during Salmonella infection, thus defining their protective qualities.

    • C. Coral Domínguez-Medina
    • , Marisol Pérez-Toledo
    •  & Adam F. Cunningham

  • Article
    | Open Access

    Protein tyrosine phosphatases regulate many cellular processes but are difficult to study in their native context. Here the authors develop an approach for using light to control the activity of a disease-relevant phosphatase without interfering with its native cellular organization.

    • Akarawin Hongdusit
    • , Peter H. Zwart
    •  & Jerome M. Fox

  • Article
    | Open Access

    Cells maintain membrane fluidity by regulating lipid saturation, but the molecular mechanisms of this homeoviscous adaptation remain poorly understood. Here authors reconstituted the core machinery for regulating lipid saturation in baker’s yeast to directly characterize its response to defined membrane environments and uncover its mode-of-action.

    • Stephanie Ballweg
    • , Erdinc Sezgin
    •  & Robert Ernst

  • Article
    | Open Access

    In voltage-gated potassium (KV) channels, the voltage-sensing domain (VSD) undergoes activation states to trigger pore opening via electro–mechanical (E–M) coupling. Here authors show that KV7.1 undergoes a two-stage E–M coupling mechanism during voltage-dependent activation.

    • Panpan Hou
    • , Po Wei Kang
    •  & Jianmin Cui

  • Article
    | Open Access

    The β1-adrenergic receptor (β1AR) is a G-protein-coupled receptor (GPCRs) that binds catecholamine ligands. Here the authors employ site-specific labelling and 19F NMR measurements to characterise the structural changes and dynamics in the cytoplasmic region of β1AR upon agonist stimulation and coupling to a Gs-protein-mimetic nanobody.

    • J. Niclas Frei
    • , Richard W. Broadhurst
    •  & Daniel Nietlispach

  • Article
    | Open Access

    KUP transporters facilitate potassium uptake by the co-transport of protons and are key players in potassium homeostasis. Here authors identify the potassium importer KimA from Bacillus subtilis as a new member of the KUP transporter family and show the cryo-EM structure of KimA in an inward-occluded, trans-inhibited conformation.

    • Igor Tascón
    • , Joana S. Sousa
    •  & Inga Hänelt

  • Article
    | Open Access

    To carry out their function, transcription factors must efficiently recognize specific DNA sequence targets, a complex problem in the context of eukaryotic chromatin. Here the authors use single-molecule biophysical experiments, statistical mechanical theory and bioinformatics analyses to conclude that interactions with non-target sequences near promoters serve to increase overall affinity and targeting efficiency.

    • Milagros Castellanos
    • , Nivin Mothi
    •  & Victor Muñoz

  • Article
    | Open Access

    Native mass spectrometry allows monitoring the folding and interactions of multiple coexisting species but its temporal resolution is traditionally limited. Here, the authors develop a temperature-jump electrospray source for mass spectrometry that enables fast kinetics experiments at different temperatures.

    • Adrien Marchand
    • , Martin F. Czar
    •  & Renato Zenobi

  • Article
    | Open Access

    TrkH is a bacterial ion channel that is regulated by nucleotides and its associated protein TrkA. Here the authors present ADP and ATP bound TrkH-TrkA structures, which reveal the mechanism for the transmission of nucleotide-induced conformational changes in TrkA to the opening of the TrkH channel and further support the proposed gating mechanism with functional studies.

    • Hanzhi Zhang
    • , Yaping Pan
    •  & Ming Zhou

  • Article
    | Open Access

    In the C. elegans zygote, (anterior) aPAR and (posterior) pPAR proteins are key to polarity maintenance, what factors determine the selection of the polarity axis remains unclear. Here authors formulate a reaction-diffusion model in realistic cell geometry and find that long-axis polarisation is promoted by cytosolic dephosphorylation at onset and its steady state determined by minimising the length of the aPAR-pPAR interface.

    • Raphaela Geßele
    • , Jacob Halatek
    •  & Erwin Frey

  • Article
    | Open Access

    Adherens junctions (AJs) mediate cell-cell adhesion between epithelial cells but tools to study their dynamic regulation are lacking. Here the authors develop an optochemical tool to stimulate the assembly of AJs through addition of a photocleavable tool and their dissociation upon exposure to light.

    • Dirk Ollech
    • , Tim Pflästerer
    •  & Elisabetta Ada Cavalcanti-Adam

  • Article
    | Open Access

    Cyanobacteria evolved carbon-concentration mechanisms to enhance the efficiency of photosynthetic CO2 fixation, but the molecular principles have remained unknown. Here authors use cryo-EM to reveal how modular adaptations enabled the photosynthetic complex I from the cyanobacterium Thermosynechococcus elongatus to concentrate CO2.

    • Jan M. Schuller
    • , Patricia Saura
    •  & Ville R. I. Kaila

  • Article
    | Open Access

    Large Clostridial toxins infiltrate host cells using a translocation domain (LCT-T). Here, using a genomics-driven approach and functional assays, the authors uncover the presence of distant LCT-T homologs in bacteria outside clostridia and provide evidence for a toxic effector function in the gammaproteobacterium Serratia marcescens.

    • Kathleen E. Orrell
    • , Michael J. Mansfield
    •  & Roman A. Melnyk

  • Article
    | Open Access

    B cell receptors (BCR) capture antigen and initiate downstream antibody responses, but whether and how BCR signaling is regulated by BCR mobility is still unclear. Here the authors show, using single molecule imaging and machine learning analyses, that BCR and CD19 mobility is modulated by the actin nucleation regulators Arp2/3 and N-WASP to control BCR signaling.

    • Ivan Rey-Suarez
    • , Brittany A. Wheatley
    •  & Arpita Upadhyaya

  • Article
    | Open Access

    In the canonical bacterial transcription, both nascent transcript and polymerase dissociate from template DNA. By employing multi-color single-molecule fluorescence imaging, here the authors show that RNA polymerases remain bound to DNA after the transcript release.

    • Timothy T. Harden
    • , Karina S. Herlambang
    •  & Jeff Gelles

  • Article
    | Open Access

    The valve-like trichomes of the desert plant Tillandsia landbeckii allow water acquisition from fog while minimising transpiration. Here, Raux et al. show that a hygroscopic cell-wall adjacent to a semi-permeable plasma membrane at the base of the trichome confers this asymmetry in water conductance.

    • Pascal S. Raux
    • , Simon Gravelle
    •  & Jacques Dumais

  • Article
    | Open Access

    The important tuberculosis drug pyrazinamide (PZA) is converted to its active form pyrazinoic acid (POA) in Mycobacterium tuberculosis (Mtb). Here the authors identify the pantothenate biosynthesis pathway enzyme aspartate decarboxylase (PanD) as the target of PZA and determine the POA bound Mtb PanD crystal structure.

    • Qingan Sun
    • , Xiaojun Li
    •  & James C. Sacchettini

  • Article
    | Open Access

    Quantifying the effect of mutations on binding free energy is important to understand protein-protein interaction (PPI). Here the authors develop a method based on yeast display and next-generation sequencing to generate quantitative binding landscapes for any PPI regardless of their Kd value.

    • Michael Heyne
    • , Niv Papo
    •  & Julia M. Shifman

  • Article
    | Open Access

    Annexins are cytoplasmic proteins, which bind to membranes exposing negatively charged phospholipids in a Ca2+-dependent manner. Here the authors use high-speed atomic force microscopy and other techniques to show that annexin-V self-assembles into highly structured lattices that lead to a membrane phase transition on PS-rich membranes.

    • Yi-Chih Lin
    • , Christophe Chipot
    •  & Simon Scheuring

  • Article
    | Open Access

    A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Here authors use cryo-EM to visualize the secretion channel complexes (CsgF-CsgG) with and without the curli substrate and provide insights into curli biogenesis.

    • Zhaofeng Yan
    • , Meng Yin
    •  & Xueming Li

  • Article
    | Open Access

    Many RNA systems possess highly ordered 3-D structures that are essential to their function. Here the authors demonstrate that the long non-coding RNA Braveheart possesses a flexible but defined 3-D structure which is remodeled upon binding the protein CNBP.

    • Doo Nam Kim
    • , Bernhard C. Thiel
    •  & Karissa Y. Sanbonmatsu

  • Article
    | Open Access

    Niemann-Pick C1 (NPC1) exports low-density-lipoprotein (LDL)-derived cholesterol from lysosomes and comporses a Sterol-Sensing Domain (SSD). Here authors report a cryo-EM structure of human NPC1 bound to itraconazole which reveals how this binding site in the center of NPC1 blocks a putative lumenal tunnel linked to the SSD.

    • Tao Long
    • , Xiaofeng Qi
    •  & Xiaochun Li

  • Article
    | Open Access

    The contraction of cardiac and skeletal muscles is regulated by Ca2+ released from the sarcoplasmic reticulum in muscle cells. Here the authors provide molecular insights into Ca2+ regulation of muscle contraction by determining the cryo-EM structures of the human cardiac muscle thin filament in the absence and presence of Ca2+.

    • Yurika Yamada
    • , Keiichi Namba
    •  & Takashi Fujii

  • Article
    | Open Access

    Torsional stress is generated during DNA replication and transcription, however, the propagation of twist in condensed chromatin is poorly understood. Here the authors measure how force and torque impact chromatin fibers and find that the fibers fold into a left-handed superhelix that can be stabilized by positive torsion, suggesting that chromatin fibers stabilize nucleosomes under torsional stress.

    • Artur Kaczmarczyk
    • , He Meng
    •  & Nynke H. Dekker

  • Article
    | Open Access

    Performing homo-FRET measurements in cells using a fluorescence microscope is challenging, especially when using high numerical aperture objective lenses. Here the authors present a method for improved homo-FRET measurements based on anisotropy changes in photoswitchable fluorescent proteins.

    • Namrata Ojha
    • , Kristin H. Rainey
    •  & George H. Patterson

  • Article
    | Open Access

    Traction force microscopy is an effective method for measuring cellular forces but it is limited by planar geometry. Here the authors develop a facile method to produce deformable hydrogel particles and a reference-free computational method to resolve surface traction forces from particle shape deformation.

    • Daan Vorselen
    • , Yifan Wang
    •  & Julie A. Theriot

  • Article
    | Open Access

    Glass transition in soft materials can be affected by the topology of constituent particles, but the detail remains elusive. Here, Smrek et al. show that the interplay between circular topology of ring polymers and their active segments generates a new state of matter, namely active topological glass.

    • Jan Smrek
    • , Iurii Chubak
    •  & Kurt Kremer

  • Article
    | Open Access

    Many intracellular pathogens mimic extracellular matrix motifs to specifically interact with the host membrane which may influences virus particle uptake. Here authors use single molecule tension sensors to reveal the minimal forces exerted on single virus particles and demonstrate that the uptake forces scale with the adhesion energy.

    • Tina Wiegand
    • , Marta Fratini
    •  & Joachim P. Spatz

  • Article
    | Open Access

    The ATP synthase has been suggested to contain the mitochondrial permeability transition pore (mPTP), which has a crucial role in cell death. Here the authors show that reconstituted ATP synthase monomers form voltage-gated and Ca2+ -activated channels with the key features of mPTP.

    • Nelli Mnatsakanyan
    • , Marc C. Llaguno
    •  & Elizabeth A. Jonas

  • Article
    | Open Access

    The ultrastructural details of the periodic scaffold of actin rings under the plasma membrane of axons remain unknown. Here, the authors combine platinum-replica electron and optical super-resolution microscopy and resolve actin rings as braids made of two long, intertwined actin filaments connected by a dense mesh of aligned spectrins.

    • Stéphane Vassilopoulos
    • , Solène Gibaud
    •  & Christophe Leterrier

  • Article
    | Open Access

    GPCRs are versatile cellular sensors for chemical stimuli but the molecular mechanisms underlying mechanically induced GPCR activation have remained elusive. Here authors identify the C-terminal helix 8 (H8) as the essential structural motif endowing H1R and other GPCRs with mechanosensitivity.

    • Serap Erdogmus
    • , Ursula Storch
    •  & Michael Mederos y Schnitzler

  • Article
    | Open Access

    Several factors contribute to the efficiency of protein expression. Here the authors show that the identity of amino acids encoded by codons at position 3–5 significantly impact translation efficiency and protein expression levels.

    • Manasvi Verma
    • , Junhong Choi
    •  & Sergej Djuranovic

Browse broader subjects

Browse narrower subjects

Browse Biophysics across other nature.com journals