Biophysical methods articles within Nature Communications

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  • Article
    | Open Access

    The organization of membrane proteins is critical to cellular function. Here the authors explore how computational protein design, MD simulation, and cell-free systems can be combined to elucidate how membrane-protein hydrophobic mismatch affects protein folding and organization in synthetic lipid membranes.

    • Justin A. Peruzzi
    • , Jan Steinkühler
    •  & Neha P. Kamat

  • Article
    | Open Access

    Studying the fluctuations of biological membranes with high resolution is challenging. Here, the authors combine metal- and graphene-induced energy transfer (MIET/GIET) with fluorescence correlation spectroscopy (FCS) to monitor such fluctuations with nanometer and microsecond resolution.

    • Tao Chen
    • , Narain Karedla
    •  & Jörg Enderlein

  • Article
    | Open Access

    Systematic understanding of CRISPR enzyme RNA binding specificity and cleavage is lacking. Here the authors report RNA chip-hybridised association-mapping platform (RNA-CHAMP), a workflow that repurposes next generation DNA sequencing chips to measure the binding affinity for RNA targets.

    • Hung-Che Kuo
    • , Joshua Prupes
    •  & Ilya J. Finkelstein

  • Article
    | Open Access

    Osmotic pressure is thought to play a key role in many cellular and developmental processes, but remains challenging to measure it in cells and tissues. Here, the authors present a sensor based on double emulsion droplets that allows quantification of osmotic pressure in situ and in vivo.

    • Antoine Vian
    • , Marie Pochitaloff
    •  & Otger Campàs

  • Article
    | Open Access

    Marin-Llaurado and colleagues engineer curved epithelial monolayers of controlled geometry and develop a new technique to map their state of stress. They show that pronounced stress anisotropies influence cell alignment.

    • Ariadna Marín-Llauradó
    • , Sohan Kale
    •  & Xavier Trepat

  • Article
    | Open Access

    The details of CRISPR-Cas target search are unresolved. Here the authors analyse the target search process of the Type I CRISPR-Cas complex Cascade: they show that target search and target recognition are tightly linked, and DNA supercoiling and limited 1D diffusion play a role.

    • Pierre Aldag
    • , Marius Rutkauskas
    •  & Ralf Seidel

  • Article
    | Open Access

    In vivo manipulation of cells has applications in cell-based therapy, tissue engineering and targeted drug delivery. Here the authors demonstrate in vivo programmable acoustic manipulation of genetically engineered bacteria using holographic acoustic tweezers.

    • Ye Yang
    • , Yaozhang Yang
    •  & Hairong Zheng

  • Article
    | Open Access

    It remains unclear how cells respond to complex extracellular geometries at the mesoscale. Here, the authors study the organization of bone cells in landscapes with varying curvatures, observing a preference for local concavities, multicellular bridging, and collective stress fiber orientation.

    • Sebastien J. P. Callens
    • , Daniel Fan
    •  & Amir A. Zadpoor

  • Article
    | Open Access

    The Hedgehog morphogen creates gradients during development, but diffusion alone cannot explain its spatiotemporal dynamics. Hedgehog transport requires binding heparan sulfate sugar chains, and the authors now show that Hedgehogs can spread by interacting with sequential heparan molecules.

    • Fabian Gude
    • , Jurij Froese
    •  & Kay Grobe

  • Article
    | Open Access

    Aromatic amino acids in proteins support ligand binding and protein stability. To parse the physiocochemical roles of aromatic interactions, here Galles, Infield and co-authors identify pyrrolysine-based aminoacyl-tRNA synthetases that enable the encoding of fluorinated phenylalanine amino acids.

    • Grace D. Galles
    • , Daniel T. Infield
    •  & Christopher A. Ahern

  • Article
    | Open Access

    In anaphase, any unresolved DNA entanglements between the segregating sister chromatids can give rise to chromatin bridges. Here, the authors present an in vitro single-molecule assay that mimics chromatin under tension, to show that PICH is a tension- and ATP-dependent nucleosome remodeler.

    • Dian Spakman
    • , Tinka V. M. Clement
    •  & Gijs J. L. Wuite

  • Perspective
    | Open Access

    Synthetic biology encompasses engineering approaches to either redesign biological organisms with new molecular abilities or build up organism from the bottom to improve our understanding of life. Here, the authors summarize current approaches that can be applied for the synthetic engineering of viral replication cycles and discuss the potential DURC risk associated with such bottom-up approaches in infectious disease.

    • Oskar Staufer
    • , Gösta Gantner
    •  & Joachim P. Spatz

  • Article
    | Open Access

    FRET can be used to study conformational changes and protein-protein interactions. Here the authors report Binary-FRET for monitoring two FRET reactions, one encoded in the fluorescence lifetime of the donor, another encoded in its anisotropy, and monitor the dynamics of CaMKII and its interaction with NR2B.

    • Tuan A. Nguyen
    • , Henry L. Puhl III
    •  & Steven S. Vogel

  • Article
    | Open Access

    Release of the ATP hydrolysis product orthophosphate (Pi) from the myosin active site is central in force generation but is poorly understood. Here, Moretto et al. present evidence for multistep Pi-release reconciling apparently contradictory results.

    • Luisa Moretto
    • , Marko Ušaj
    •  & Alf Månsson

  • Article
    | Open Access

    The authors introduce photonic force optical coherence elastography that uses a light-sheet for parallelised and localised mechanical loading. They demonstrate the combination of 3D imaging of extracellular matrix mechanics with cellular-scale resolution and dynamic monitoring of cell-mediated changes.

    • Yuechuan Lin
    • , Nichaluk Leartprapun
    •  & Steven G. Adie

  • Article
    | Open Access

    Drosophila mesoderm invagination begins with the formation of a furrow. Here they show that a long-range mechanism, powered by actomyosin contraction between the embryo polar caps, works like a ‘cheese-cutter wire’ indenting the tissue surface and folding it into a propagating furrow.

    • Julien Fierling
    • , Alphy John
    •  & Matteo Rauzi

  • Article
    | Open Access

    TMEM16A, a calcium-activated chloride channel involved in multiple cellular processes, is implicated in various diseases, but its pharmacology remains poorly understood. Here, the authors combine cryo-EM and electrophysiology to elucidate the mechanism of TMEM16A inhibition by the pore blocker 1PBC.

    • Andy K. M. Lam
    • , Sonja Rutz
    •  & Raimund Dutzler

  • Article
    | Open Access

    Gasdermin-A3 pore formation propagates along diverse pathways. It begins with membrane attachment and oligomeric pre-assembly. Once inserted in the membrane, the oligomers re-assemble into various shapes and sizes, which open their lytic pores.

    • Stefania A. Mari
    • , Kristyna Pluhackova
    •  & Daniel J. Müller

  • Article
    | Open Access

    RecBCD is a remarkably fast DNA helicase. Using a battery of biophysical methods, Zananiri et. al reveal additional, non-catalytic ATP binding sites that increase the ATP flux to the catalytic sites that allows fast unwinding when ATP is scarce.

    • Rani Zananiri
    • , Sivasubramanyan Mangapuram Venkata
    •  & Arnon Henn

  • Article
    | Open Access

    Ultrasound can be used to non-invasively control neuronal functions. Here the authors report the use of human Transient receptor potential ankyrin 1 (hsTRPA1) to achieve ultrasound sensitivity in mammalian cells, and show that it can be used to manipulate neurons in the mammalian brain.

    • Marc Duque
    • , Corinne A. Lee-Kubli
    •  & Sreekanth H. Chalasani

  • Article
    | Open Access

    Here the authors probe the cleavage and gate opening of single-stranded DNA by the human topoisomerase TRR using a unique single-molecule strategy to reveal structural plasticity in response to both double-stranded DNA and the helicase BLM.

    • Julia A. M. Bakx
    • , Andreas S. Biebricher
    •  & Erwin J. G. Peterman

  • Article
    | Open Access

    The insertion and folding nascent or fully synthesized polypeptides into membranes is assisted by insertases. Here, the authors use a range of biophysical approaches to provide molecular details of how the transmembrane insertase YidC facilitates the insertion a protein into a phospholipid membrane.

    • Pawel R. Laskowski
    • , Kristyna Pluhackova
    •  & Daniel J. Müller

  • Article
    | Open Access

    UvrD is a model helicase from the non-hexameric Superfamily 1. Here, the authors use optical tweezers to measure directly the stepwise translocation of UvrD along a DNA hairpin, and propose a mechanism in which UvrD moves one base pair at a time, but sequesters the nascent single strands, releasing them after a variable number of ATP hydrolysis cycles.

    • Sean P. Carney
    • , Wen Ma
    •  & Yann R. Chemla

  • 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

    Current methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) that form metastases have several limitations. Here, the authors show an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts.

    • Bashar Hamza
    • , Alex B. Miller
    •  & Scott R. Manalis

  • Article
    | Open Access

    Photosynthetic Complex I (PS-CI) is proposed to couple ferredoxin oxidation and plastoquinone reduction to proton pumping across thylakoid membranes. Here the authors determine the reduction potentials of the iron-sulphur clusters of PS-CI and thus the bioenergetics of the electron transfer relay.

    • Katherine H. Richardson
    • , John J. Wright
    •  & Maxie M. Roessler

  • Article
    | Open Access

    Light-driven micromotors can convert energy to motion in sub-millimeter dimensions. Here, the authors extend this concept and introduce reconfigurable micromachines with multiple components, driven by optoelectronic tweezers, and demonstrate new functionalities.

    • Shuailong Zhang
    • , Mohamed Elsayed
    •  & Aaron R. Wheeler

  • 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

    Mechanical forces, along with gene regulatory networks and cell-cell signalling, play an important role in the complex organization of tissues. Here the authors describe devices that actively apply mechanical force to developing neural tube, demonstrating that mechanical forces increase growth and enhance patterning.

    • Abdel Rahman Abdel Fattah
    • , Brian Daza
    •  & Adrian Ranga

  • Article
    | Open Access

    While rheology studies have contributed to the understanding of the viscoelastic properties of living cells, the use of higher frequencies promises elucidate the link between cellular and molecular properties. Here authors introduce a rheological assay that measures the cell mechanical response across a continuous frequency range ≈ 1 – 40 kHz.

    • Gotthold Fläschner
    • , Cosmin I. Roman
    •  & Daniel J. Müller

  • Article
    | Open Access

    Synaptic loss may disturb the excitatory to inhibitory balance (E/I ratio) in circuits vulnerable in Alzheimer’s disease (AD). The authors find reduced synaptic levels of PSD-95 and gephyrin and show that individuals with AD exhibit a pro-excitatory shift of postsynaptic densities and the electrophysiological synaptic E/I ratio in the parietal cortex.

    • Julie C. Lauterborn
    • , Pietro Scaduto
    •  & Agenor Limon

  • 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

    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

    The GntR superfamily is one of the largest families of transcription factors in prokaryotes. Here the authors combine biophysical analysis and structural biology to dissect the mechanism by which NanR — a GntR-family regulator — binds to its promoter to repress the transcription of genes necessary for sialic acid metabolism.

    • Christopher R. Horne
    • , Hariprasad Venugopal
    •  & Renwick C. J. Dobson

  • Article
    | Open Access

    Here Arndt et al. establish rotating-crystal magneto-optical detection (RMOD) as a near-point-of-care diagnostic tool for malaria detection and report a sensitivity and specificity of 82% and 84%, respectively, as validated by analyzing a clinical population in a high transmission setting in Papua New Guinea.

    • L. Arndt
    • , T. Koleala
    •  & S. Karl

  • Article
    | Open Access

    Patch clamp recording of neurons is slow and labor-intensive. Here the authors present a method for automated deep learning driven label-free image guided patch clamp physiology to perform measurements on hundreds of human and rodent neurons.

    • Krisztian Koos
    • , Gáspár Oláh
    •  & Peter Horvath

  • Article
    | Open Access

    Mechanical strength of in situ assembled nuclear lamin filaments arranged in a 3D meshwork is unclear. Here, using mechanical, structural and simulation tools, the authors report the hierarchical organization of the lamin meshwork that imparts strength and toughness to lamin filaments at par with silk and Kevlar®

    • K. Tanuj Sapra
    • , Zhao Qin
    •  & Ohad Medalia

  • Article
    | Open Access

    Existing tools to study hearing are limited. Here the authors report Bio-OptoAcoustic (BOA) stimulation wherein they use optical forces to generate localised sound and activate the auditory system of zebrafish larvae.

    • Itia A. Favre-Bulle
    • , Michael A. Taylor
    •  & Ethan K. Scott

  • 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

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