Nanoscale biophysics articles within Nature Communications

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  • Article
    | Open Access

    Single molecule investigations are often performed in fluidic environments, but molecular diffusion and limited photon counts can compromise studies of processes with fast or slow dynamics. The authors introduce a planar optofluidic antenna which enhances the fluorescence signal from molecules, applicable to a diverse range of studies.

    • Luis Morales-Inostroza
    • , Julian Folz
    •  & Vahid Sandoghdar
  • Article
    | Open Access

    A new carbonate phase calcium carbonate hemihydrate was recently discovered and characterized, but exclusively as a synthetic material. Here the authors find that it exists in nature, albeit transiently, on the surface of growing nacre and coral skeletons, and show that 2 amorphous and 2 metastable crystalline nano-minerals form before biominerals settle into their stable crystals.

    • Connor A. Schmidt
    • , Eric Tambutté
    •  & Pupa U.P.A. Gilbert
  • Article
    | Open Access

    There is increasing interest in measuring the mechanical properties of living cells. Here, the authors develop a method to simultaneously measure the cell mass and two parameters related to its natural oscillation or resonance frequencies.

    • Sophie Herzog
    • , Gotthold Fläschner
    •  & Daniel J. Müller
  • Article
    | Open Access

    Photolabeling of intracellular molecules is an invaluable approach to study multiple cellular processes. Here, the authors report on the near-infrared to far-red photoconversion in the miRFP family of fluorescent proteins, which enables photolabeling entirely performed in the near-infrared range.

    • Francesca Pennacchietti
    • , Jonatan Alvelid
    •  & Ilaria Testa
  • Article
    | Open Access

    β-actin and γ-actin are nearly identical, and yet incorporate into different cytoskeletal structures. Here, the authors create isoform-pure reconstituted networks and study their structural and mechanical differences, underscoring the significance of the isoforms in diverse cellular functions.

    • Peter Nietmann
    • , Kevin Kaub
    •  & Andreas Janshoff
  • Article
    | Open Access

    Understanding the topological arrangement and transition dynamics of mesoscale assemblies is complicated by their molecular complexity. Here, the authors use DNA origami nanosprings to show that mesoscale helical handedness is dictated by backbone torque rather than achiral orientation.

    • Deepak Karna
    • , Eriko Mano
    •  & Hanbin Mao
  • Article
    | Open Access

    Nano-environmental probes and advance imaging microscopy provide deep insight into protein phase separation and the interaction of condensates with membranes, revealing that wetting by condensates can modulate membrane lipid packing and hydration.

    • Agustín Mangiarotti
    • , Macarena Siri
    •  & Rumiana Dimova
  • Article
    | Open Access

    The soft-grainy microstructure of cooked egg yolk is the result of a series of out of equilibrium processes of its protein-lipid contents. Here, the authors develop a time-temperature phase diagram that shows the coupling of the nanoscale processes that result in the grainy-gel microstructure of cooked egg yolk.

    • Nimmi Das Anthuparambil
    • , Anita Girelli
    •  & Christian Gutt
  • Article
    | Open Access

    Fibrous networks constructed from high aspect ratio protein building blocks are ubiquitous in nature, but the functional advantage of such building blocks over globular proteins is not understood. Here, using shear rheology and small-angle neutron scattering, the authors characterise the mechanical and structural properties of photochemically crosslinked protein L and fibrin networks and show that aspect ratio is a crucial property that defines network architecture and mechanics.

    • Matt D. G. Hughes
    • , Sophie Cussons
    •  & Lorna Dougan
  • Article
    | Open Access

    Tailed bacteriophages account for the majority of all phages. Here, the authors employ cryo-EM and structure prediction techniques to investigate the atomic structure of the R4C phage capsid and the in- situ structure of its unique long rigid tail.

    • Yang Huang
    • , Hui Sun
    •  & Ningshao Xia
  • Article
    | Open Access

    The organization of proteins and sugars on the cell membrane is crucial for cell signaling and function. Here, authors develop molecular probes and simulations to characterize the spatial organization of macromoleucles on live cell membranes.

    • Daniel P. Arnold
    • , Yaxin Xu
    •  & Sho C. Takatori
  • Article
    | Open Access

    Collagen is an important structural protein in connective tissue, but the effect of location and type of micro-ruptures in the structure on the overall tissue is not well understood. Here, the authors use scale-bridging simulations to determine the breakage points in collagen, and how the failure mode helps to prevent material ageing

    • Benedikt Rennekamp
    • , Christoph Karfusehr
    •  & Frauke Gräter
  • Article
    | Open Access

    Immobilization of biomolecules into porous materials could lead to enhanced performance in terms of stability and easier separation for their reuse. Here authors gain insights into the spatial arrangement of green fluorescent protein entrapped in a mesoporous MOF by situ small-angle neutron scattering.

    • Xiaoliang Wang
    • , Lilin He
    •  & Shengqian Ma
  • Article
    | Open Access

    Electron transfer between mitochondrial cytochrome c and subunit of cytochrome bc1 can proceed at long distance. Here the authors investigate further the mechanism and show phosphorylation regulation of the interactions between the protein partners in the electron transport chain.

    • Alexandre M. J. Gomila
    • , Gonzalo Pérez-Mejías
    •  & Anna Lagunas
  • Article
    | Open Access

    DNA origami can be coated in a layer of silica to improve chemical and thermal stability however; it is unclear if this is a surface or interpenetrating layer. Here, the authors use in situ small-angle X-ray scattering to study silica deposition and observe internal silica formation resulting in DNA origami condensation and structure shrinkage.

    • Martina F. Ober
    • , Anna Baptist
    •  & Bert Nickel
  • Article
    | Open Access

    Studies on mechanotransduction are limited by our ability to apply low range forces to specific mechanoreceptors on cell membranes. Here the authors report the Nano-winch, a programmable DNA origami-based molecular actuator, to manipulate multiple mechanoreceptors in parallel by exerting piconewton forces.

    • A. Mills
    • , N. Aissaoui
    •  & G. Bellot
  • Article
    | Open Access

    Understanding and controlling the rheology of polymeric complex fluids is of fundamental importance in both industry and biology. Here, Michieletto et al. show how to achieve time-dependent rheology of DNA solutions via enzymatically-driven architectural alterations by restriction endonucleases.

    • D. Michieletto
    • , P. Neill
    •  & R. M. Robertson-Anderson
  • Article
    | Open Access

    SAP97/hDLG is a ubiquitous, alternatively spliced, and conserved modular scaffolding protein involved in the organization cell junctions and excitatory synapses. Here, authors confirm that SAP97/hDLG condenses in to nanosized molecular domains in both heterologous cells and hippocampal pyramidal neurons. Authors demonstrate that in vivo and in vitro condensation, molecular signatures of nanoscale condensates and exchange kinetics of SAP97/hDLG is modulated by the local availability of alternatively spliced isoforms. Additionally, SAP97/hDLG isoforms exhibits a differential sensitivity to Ca2+ bound Calmodulin, resulting in altered properties of nanocondensates and their real-time regulation

    • Premchand Rajeev
    • , Nivedita Singh
    •  & Deepak Nair
  • Article
    | Open Access

    Actin filaments generate force in diverse contexts, although how they can produce nanonewtons of force is unclear. Here, the authors apply cryo-electron tomography, quantitative analysis, and modelling to reveal the podosome core is a dense, spring-loaded, actin network storing elastic energy.

    • Marion Jasnin
    • , Jordan Hervy
    •  & Renaud Poincloux
  • Article
    | Open Access

    Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.

    • Chad R. Simmons
    • , Tara MacCulloch
    •  & Hao Yan
  • Article
    | Open Access

    MUC1 is a heavily glycosylated protein on the cell surface. Here the authors show that MUC1 prefers negative over positive membrane curvature due to its bulky size, enabling MUC1 to avoid endocytosis and surface removal based on curvature preference.

    • Chih-Hao Lu
    • , Kayvon Pedram
    •  & Bianxiao Cui
  • Article
    | Open Access

    Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.

    • Lauren S. Lastra
    • , Y. M. Nuwan D. Y. Bandara
    •  & Kevin J. Freedman
  • Article
    | Open Access

    Artificial systems to control the transport of molecules across biomembranes can be useful for biosensing or drug delivery. Here, the authors assemble a DNA channel enabling the precisely timed, stimulus-controlled transport of functional proteins across bilayer membranes.

    • Swarup Dey
    • , Adam Dorey
    •  & Hao Yan
  • Article
    | Open Access

    The authors show how tubular surface structures in all cell types, have the ability to twist and perform rotary sweeping motion to explore the extracellular environment. This has implications for migration, sensing and cell communication.

    • Natascha Leijnse
    • , Younes Farhangi Barooji
    •  & Poul Martin Bendix
  • Article
    | Open Access

    The permeability barrier of nuclear pores is formed by disordered and yet self-interacting FG repeat domains, whose sequence heterogeneity is a challenge for mechanistic insights. Here the authors overcome this challenge and characterize the protein’s dynamics by applying NMR techniques to an FG phase system that has been simplified to its essentials.

    • Eszter E. Najbauer
    • , Sheung Chun Ng
    •  & Loren B. Andreas
  • Article
    | Open Access

    The actin-based molecular motors, myosins, have also been linked to transcription, but their precise role has remained elusive. Here the authors show RNA polymerase II (RNAPII) is lost from chromatin upon myosin perturbation and that myosin acts as a molecular anchor to maintain RNAPII spatial organisation.

    • Yukti Hari-Gupta
    • , Natalia Fili
    •  & Christopher P. Toseland
  • Article
    | Open Access

    Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.

    • Lauren Ashley Mayse
    • , Ali Imran
    •  & Liviu Movileanu
  • Article
    | Open Access

    Developing hydrolytic nanozymes remains challenging. Here the authors present a rational methodology to design hydrolytic nanozyme by developing a data-informed strategy to screen and identify potential scaffold and active sites of hydrolase-like nanozyme.

    • Sirong Li
    • , Zijun Zhou
    •  & Hui Wei
  • Article
    | Open Access

    Developing antibacterial agents which don’t have cytotoxic effects against mammalian cells is of interest for biomedical applications. Here, the authors explore how attaching inert polymer brushes to different sized nanoparticles can result in toxicity to bacteria but not to mammalian cells in a size dependent manner.

    • Yunjiang Jiang
    • , Wan Zheng
    •  & Hongjun Liang
  • Article
    | Open Access

    Here, the authors combine single-molecule atomic force spectroscopy measurements and molecular dynamics simulations to investigate the binding of spike proteins from four SARS-CoV-2 variants of concern (VoC) to the human ACE2 receptor. They observe an increase in the RBD-ACE2 complex stability for several of the VoCs and derive how the mutations affect the kinetic, thermodynamic and structural properties of complex formation.

    • Melanie Koehler
    • , Ankita Ray
    •  & David Alsteens
  • Article
    | Open Access

    The concentration of a biomarker in solution can be determined by counting single molecules. Here the authors report a digital immunoassay scheme with solid-state nanopore readout to quantify a target protein and use this to measure thyroid-stimulating hormone from human serum.

    • Liqun He
    • , Daniel R. Tessier
    •  & Vincent Tabard-Cossa
  • Article
    | Open Access

    The authors have recently developed molecular force microscopy (MFM) which uses fluorescence polarisation to measure cell-surface receptor force orientation. Here they show that structured illumination microscopes, which inherently use fluorescence polarisation, can be used for MFM in a turn-key manner.

    • Aaron Blanchard
    • , J. Dale Combs
    •  & Khalid Salaita
  • Article
    | Open Access

    High-speed atomic force microscopy height spectroscopy and single channel electrophysiology recordings are used to correlate conformational and functional dynamics of the model membrane protein, outer membrane protein G (OmpG). These techniques show that both states coexist and rapidly interchange in all conditions supported by molecular dynamics simulations.

    • Raghavendar Reddy Sanganna Gari
    • , Joel José Montalvo‐Acosta
    •  & Simon Scheuring
  • Article
    | Open Access

    Molecular scale force application in physiological environments is important for studying mechanotransduction. Here, the authors use a molecular machine to apply forces at cell-matrix and cell-cell junctions using light to trigger twisting actuation which then pulls on cell membrane receptors.

    • Yijun Zheng
    • , Mitchell K. L. Han
    •  & Aránzazu del Campo
  • 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

    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