Nanoscale biophysics articles within Nature Communications

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  • 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

    Muscle cells express an adhesion molecule called metavinculin, which has been associated with cardiomyopathies. Here, the authors employed molecular tension sensors to reveal that metavinculin expression modulates cell adhesion mechanics and they develop a mouse model to demonstrate that the presence of metavinculin is not as critical for heart muscle function as previously thought.

    • Verena Kanoldt
    • , Carleen Kluger
    •  & Carsten Grashoff

  • Article
    | Open Access

    High-speed atomic force imaging allows for the visualisation of molecular‐level activity in real-time. Here, the authors use HS-AFM to image the activity of an antimicrobial peptide on a membrane and are able to detect previously unknown molecular mechanisms behind its action.

    • Francesca Zuttion
    • , Adai Colom
    •  & Ignacio Casuso

  • Article
    | Open Access

    Septins are GTP-binding proteins involved in diverse cellular processes including division, polarity maintenance and membrane remodeling. Here authors use high-speed atomic force microscopy to show that assembly of septin filaments is a diffusion-driven process, while septin assembly into higher-order involves septin self-templating

    • Fang Jiao
    • , Kevin S. Cannon
    •  & Simon Scheuring

  • Article
    | Open Access

    Determining molecular clustering in Photoactivated Localization Microscopy (PALM) experiments requires knowledge of the blinking properties of the fluorophore to prevent overcounting artefacts. Here the authors develop an experimental and analytical framework to determine the blinking parameters of fluorophores and incorporate this information into cluster analysis.

    • René Platzer
    • , Benedikt K. Rossboth
    •  & Mario Brameshuber

  • Article
    | Open Access

    Understanding the biological identity of nanoparticles has mainly focused on the hard protein corona with the soft corona largely overlooked. Here, using click-chemistry, the authors report on a capture system for the identification of the soft corona proteins and investigate the effects on cell interactions.

    • Hossein Mohammad-Beigi
    • , Yuya Hayashi
    •  & Duncan S. Sutherland

  • Article
    | Open Access

    The authors test expansion microscopy protocols for investigation of the molecular organisation of mammalian synaptonemal complexes (SCs) with structured illumination microscopy. They show that the molecular structure is preserved during expansion and ultrastructural details of SCs can be revealed.

    • Fabian U. Zwettler
    • , Marie-Christin Spindler
    •  & Markus Sauer

  • Article
    | Open Access

    While infrared nanospectroscopy methods based on thermomechanical detection (AFM-IR) enables the acquisition of absorption spectra at the nanoscale, single molecule detection has not been possible so far. Here, the authors present off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR), which allows measuring infrared absorption spectra at the single molecule level in a time scale of seconds with high throughput and demonstrate that the secondary structure of single protein molecules can be determined with this method.

    • Francesco Simone Ruggeri
    • , Benedetta Mannini
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. Here, the authors use a DNA origami-based force clamp to investigate the assembly dynamics of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under pico newton forces.

    • Kevin Kramm
    • , Tim Schröder
    •  & Dina Grohmann

  • Article
    | Open Access

    Some kinesins exhibit off-axis power strokes but their impact on motility and force generation in microtubule overlaps has not been investigated so far. Here authors use a 3D in vitro motility assay and find that Ndc’s off-axis motor forces generate torque in antiparallel microtubules which causes microtubule twisting and coiling.

    • Aniruddha Mitra
    • , Laura Meißner
    •  & Stefan Diez

  • Article
    | Open Access

    Near-infrared (NIR) fluorophores have attracted interest for bioimaging; yet availability, biocompatibility and application can be an issue. Here, the authors report on the development of Egyptian Blue nanosheets with high NIR fluorescence and photostability demonstrating bioimaging applications in vivo.

    • Gabriele Selvaggio
    • , Alexey Chizhik
    •  & Sebastian Kruss

  • Article
    | Open Access

    Nature has developed the ability to produce a wide range of optical effects most notably in the butterfly wing. Here, the authors report on the analysis of the structures responsible for ultra-black coloration across different butterflies and combine this with modelling to identify the key characteristics

    • Alexander L. Davis
    • , H. Frederik Nijhout
    •  & Sönke Johnsen

  • 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

    Current methods to measure extracellular pH are often limited in resolution and response times. Here the authors present a label-free nanoprobe, consisting of a zwitterionic nanomembrane at the tip of a nanopipette, which enables high spatiotemporal resolution pH measurements and topography-pH 3D mapping in live cancer cells.

    • Yanjun Zhang
    • , Yasufumi Takahashi
    •  & Yuri Korchev

  • Article
    | Open Access

    Biology serves as inspiration in materials development; this requires improved understanding of the surface chemistry responsible for processes which are being mimicked. Here, the authors report on the use of near edge X-ray absorption fine structure (NEXAFS) imaging to analyze the surface chemistry of insect cuticle.

    • Joe E. Baio
    • , Cherno Jaye
    •  & Tobias Weidner

  • Article
    | Open Access

    The interaction between proteins and nanomaterials is complex and of interest for controlling nanoparticle fate. Here, using experimental and computational methods, the authors report on the effect of hydroxyl groups on protein interaction and how they can be used to enhance circulation times.

    • Xiang Lu
    • , Peipei Xu
    •  & Yu-Qiang Ma

  • Article
    | Open Access

    Nanopore microscopy is capable of detecting knots in DNA polymers, a common structural feature. Here the authors show nanopore sensors can map the equilibrium structure of these knots between tight and loose states.

    • Rajesh Kumar Sharma
    • , Ishita Agrawal
    •  & Slaven Garaj

  • Article
    | Open Access

    The reovirus outercapsid protein σ1 binds to α-linked sialic acid and junctional adhesion molecule A (JAM-A) for virus entry. Here, combining atomic force microscopy and confocal microscopy, the authors provide insights into the dynamics of these interactions at the single-virion level in living cells.

    • Melanie Koehler
    • , Pavithra Aravamudhan
    •  & David Alsteens

  • Article
    | Open Access

    Light-up aptamers are widely used for fluorescence visualization of non-coding RNA in vivo. Here the authors employ single-molecule fluorescence-force spectroscopy to characterize the mechanical responses of the G-Quadruplex based light-up aptamers Spinach2, iMangoIII and MangoIV, which is of interest for the development of improved fluorogenic modules for imaging applications.

    • Jaba Mitra
    •  & Taekjip Ha

  • Article
    | Open Access

    Sequential acquisition and image reconstruction in super-resolved structured illumination microscopy (SR-SIM) is time-consuming. Here the authors optimise both acquisition and reconstruction software to achieve multicolour SR-SIM at video frame-rates with reconstructed images displaying with only milliseconds delay during the experiment.

    • Andreas Markwirth
    • , Mario Lachetta
    •  & Marcel Müller

  • Article
    | Open Access

    The intrinsic inhomogeneity of polymer networks is masked by the usual ensemble-averaged measurements. Here the authors construct direct maps of crosslinks in an actin network by selective labeling the crosslinks with fluorescent markers and characterize the local elasticity and cross-correlation between crosslinks.

    • Lingxiang Jiang
    • , Qingqiao Xie
    •  & Steve Granick

  • Article
    | Open Access

    Bacteria assemble the surface layer (S-layer), a crystalline protein coat surrounding the curved surface, using protein self-assembly. Here authors image native and purified RsaA, the S-layer protein from C. crescentus, and show that protein crystallization alone is sufficient to assemble and maintain the S-layer in vivo.

    • Colin J. Comerci
    • , Jonathan Herrmann
    •  & W. E. Moerner

  • Article
    | Open Access

    Cellular uptake of nanoparticles is highly variable between individual cells in a population. Here, the authors show that this heterogeneity is a result of varying numbers of nanoparticle-containing endosomes while the nanoparticle dose per endosome remains constant.

    • Paul Rees
    • , John W. Wills
    •  & Huw D. Summers

  • Article
    | Open Access

    The membrane attack complex (MAC) is a hetero-oligomeric protein assembly that kills pathogens by perforating their cell envelopes. Here, the authors use atomic force microscopy to show that MAC proteins oligomerize within the membrane, allowing them to identify the kinetic bottleneck of MAC formation.

    • Edward S. Parsons
    • , George J. Stanley
    •  & Bart W. Hoogenboom

  • Article
    | Open Access

    The determination of entropy production from experimental data is a challenge but a recently introduced theoretical tool, the thermodynamic uncertainty relation, allows one to infer a lower bound on entropy production. Here the authors provide a critical assessment of the practical implementation of this tool.

    • Junang Li
    • , Jordan M. Horowitz
    •  & Nikta Fakhri

  • Article
    | Open Access

    The search for peroxidase-like as well as other enzyme-like nanozymes mainly relies on trial-and-error strategies, due to the lack of predictive descriptors. Here, the authors fill this gap by investigating the occupancy of eg orbitals as a possible descriptor for the peroxidase-like activity of transition metal oxide nanozymes

    • Xiaoyu Wang
    • , Xuejiao J. Gao
    •  & Hui Wei

  • Article
    | Open Access

    Electron transport chains rely on interactions between redox proteins, but the distance-dependence of the electron transfer rate through the solution is unknown. Here, the authors show that the current between two redox protein partners occurs at long distances and is electrochemically gated.

    • Anna Lagunas
    • , Alejandra Guerra-Castellano
    •  & Pau Gorostiza

  • Article
    | Open Access

    A known limitation of super-resolution STED microscopy is the need of high laser power which can cause photobleaching and phototoxicity. Here the authors further optimize this method and show that modulating STED intensity during acquisition results in an enhanced resolution and reduced background.

    • Maria J. Sarmento
    • , Michele Oneto
    •  & Luca Lanzanò

  • Article
    | Open Access

    Natriuretic peptides (NPs) are important hormones that regulate cardiovascular physiology by increasing cGMP levels in cardiomyocytes. Here the authors use scanning ion conductance microscopy and a cGMP FRET sensor to identify a differential localisation pattern for the natriuretic peptide receptors within the heart.

    • Hariharan Subramanian
    • , Alexander Froese
    •  & Viacheslav O. Nikolaev

  • Article
    | Open Access

    Kinesin-14s, such as Ncd, interact with microtubules with their non-processive motor domains and their diffusive tail domains, but the influence of the tail domains on motor performance is not known. Here the authors show that tail domain slippage limits the velocities and forces generated by Ncd, suggesting it acts as a slippery crosslinker.

    • Annemarie Lüdecke
    • , Anja-Maria Seidel
    •  & Stefan Diez

  • Article
    | Open Access

    BAR domain proteins feature a “banana-like” shape which is thought to aid membrane scaffolding and membrane tubulation. Here authors use DNA origami mimicking BAR domains, giant unilamellar vesicles and fluorescence imaging to study how different BAR domain shapes bind and deform membranes.

    • Henri G. Franquelim
    • , Alena Khmelinskaia
    •  & Petra Schwille

  • Article
    | Open Access

    Self-propelled molecular entities enable studying swarm behavior on a macroscopic scale but programmability of interactions has yet not been achieved. Here the authors show reversible regulation of DNA-functionalized microtubules by DNA signals and switching between solitary and swarm behaviour by employing photoresponsive DNA strands.

    • Jakia Jannat Keya
    • , Ryuhei Suzuki
    •  & Akira Kakugo

  • Article
    | Open Access

    Nanoparticle elasticity is thought to play an important role in drug delivery, but is little studied. Here, the authors use nanolipogels with tunable moduli to study the effect of particle elasticity on in vitro cellular uptake and in vivo tumor uptake, finding that stiffer particles are not as easily internalized.

    • Peng Guo
    • , Daxing Liu
    •  & Marsha A. Moses

  • Article
    | Open Access

    Excitons in light-harvesting complexes are known to significantly improve solar energy harnessing. Here, the authors investigate and explain extreme robustness against temperature of excitons in purple photosynthetic bacteria.

    • Margus Rätsep
    • , Renata Muru
    •  & Arvi Freiberg

  • Article
    | Open Access

    Eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that exist at the kilo-megabase scale. Here Cattoni et al. combine super-resolution microscopy with DNA-labeling methods to quantify absolute frequencies of interactions within TADs.

    • Diego I. Cattoni
    • , Andrés M. Cardozo Gizzi
    •  & Marcelo Nollmann

  • Article
    | Open Access

    The measurement of molecular diffusion at sub-diffraction scales has been achieved in 2D space using STED-FCS, but an implementation for 3D diffusion is lacking. Here the authors present an analytical approach to probe diffusion in 3D space using STED-FCS and measure the diffusion of EGFP at different spatial scales.

    • Luca Lanzanò
    • , Lorenzo Scipioni
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    Although DNA nanopores are widely explored as synthetic membrane proteins, it is still unclear how the anionic DNA assemblies stably reside within the hydrophobic core of a lipid bilayer. Here, the authors use molecular dynamics simulations to reveal the key dynamic interactions and energetics stabilizing the nanopore-membrane interaction.

    • Vishal Maingi
    • , Jonathan R. Burns
    •  & Mark S. P. Sansom

  • Article
    | Open Access

    Nanoscopy of non-adherent cells is currently not possible, due to their movement in solution. Here the authors immobilize and manipulate fixedE. coli by multiple optical traps; their holographic optical tweezers enable dSTORM imaging of orthogonal planes via 3D realignment of the sample.

    • Robin Diekmann
    • , Deanna L. Wolfson
    •  & Thomas Huser

  • Article
    | Open Access

    Many super-resolution imaging techniques use fluorescence emission intensity to obtain precise positional information, but other spectral information is ignored. Here, the authors develop a method that records the spectrum and position of single dye molecules to map the hydrophobicity of a surface.

    • Marie N. Bongiovanni
    • , Julien Godet
    •  & Steven F. Lee

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