Single-molecule biophysics articles within Nature Communications

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  • Article
    | Open Access

    Single-particle tracking PALM (sptPALM) provides quantitative information in vivo if the protein of interest remains in a single diffusional state during track acquisition. Here the authors develop a custom-built sptPALM microscope and a Monte-Carlo based diffusion distribution analysis to study dynamic DNA-dCas9 interactions in live bacteria.

    • Koen J. A. Martens
    • , Sam P. B. van Beljouw
    •  & Johannes Hohlbein

  • Article
    | Open Access

    Single-molecule localization microscopy (SMLM) requires the use of fluorophores with specific sets of properties. Here the authors employ conventional BODIPY dyes as SMLM fluorophores by making use of rarely reported red-shifted ground state BODIPY dimers to image fatty acids, lipid droplets and lysosomes at single-molecule resolution.

    • Santosh Adhikari
    • , Joe Moscatelli
    •  & Elias M. Puchner

  • Article
    | Open Access

    The cytoplasmic motor protein dynein senses directional tension; its microtubule-binding domains bind microtubules more strongly when under backward load. Here the authors use optical tweezers to show that the linker, buttress, and stalk domains together regulate directional tension-sensing.

    • Lu Rao
    • , Florian Berger
    •  & Arne Gennerich

  • Article
    | Open Access

    Expression of genetically encoded antibodies for cell labelling is often limited by folding issues. Here, the authors engineer an anti-HA scFv antibody that works in the cellular environment and use it to track mRNA translation dynamics in living cells and to label proteins in live zebrafish embryos.

    • Ning Zhao
    • , Kouta Kamijo
    •  & Timothy J. Stasevich

  • Article
    | Open Access

    Existing methods for protein polymer engineering suffer from low efficiency especially for synthesis large size polyproteins. Here, Deng et al. construct homo-polymer and co-polymer up to decamer by stepwise ligation and cleavage validated by atomic force microscopy-based single-molecule force spectroscopy.

    • Yibing Deng
    • , Tao Wu
    •  & Peng Zheng

  • 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

    The kinesin-3 KIF1C transports dense core vesicles in neurons and delivers integrins to cell adhesions sites. Here the authors show that KIF1C's autoinhibitory interactions are released upon binding of protein tyrosine phosphatase PTPN21 or cargo adapter Hook3 resulting in cargo-activated transport.

    • Nida Siddiqui
    • , Alexander James Zwetsloot
    •  & Anne Straube

  • Article
    | Open Access

    Translation termination is under strong selection pressure for high speed and accuracy. Here the authors provide a 3D view of the dynamics of a translating bacterial ribosome as it recruits a class-1 release factor (RF1 or RF2) upon encountering a stop codon, and propose a structure-based kinetic model for the early steps in bacterial translation termination.

    • Ziao Fu
    • , Gabriele Indrisiunaite
    •  & Joachim Frank

  • Article
    | Open Access

    How the eukaryotic helicase unzips DNA during replication is not well understood. By measuring the real-time motion of purified CMG unwinding DNA with magnetic tweezers, the authors reveal the dynamics where isolated CMG unwinds via a biased random walk with proclivity to pause.

    • Daniel R. Burnham
    • , Hazal B. Kose
    •  & Hasan Yardimci

  • Article
    | Open Access

    DHX36 is a G-quadruplex (G4) resolving helicase that targets both DNA-G4 and RNA-G4. Here the authors use single molecule FRET measurements and show that DHX36 resolves RNA-G4 structures by a mechanism involving an ATP-dependent, highly repetitive and stepwise refolding of RNA-G4 that differs from its DNA-G4 structures resolving mechanism.

    • Ramreddy Tippana
    • , Michael C. Chen
    •  & Sua Myong

  • Article
    | Open Access

    Nanopore detection of small molecules can be improved using molecular carriers, but separating a small analyte from the carrier signal can be challenging. Here the authors address this challenge using simultaneous electrical and optical readout in nanopore sensing to detect small molecules and quantify binding affinities.

    • Shenglin Cai
    • , Jasmine Y. Y. Sze
    •  & Joshua B. Edel

  • Article
    | Open Access

    Chromatin remodelling enzymes (remodellers) regulate DNA accessibility of eukaryotic genomes, which rely in large part on an ability to reposition nucleosomes. Here the authors use three-colour single-molecule FRET to simultaneously monitor remodeller-induced DNA movements on both sides of the nucleosome in real-time.

    • Anton Sabantsev
    • , Robert F. Levendosky
    •  & Sebastian Deindl

  • Article
    | Open Access

    Yeast’s Sen1 helicase is involved in the suppression of antisense transcription from bidirectional eukaryotic promoters. Here authors develop and utilize a quantitative single-molecule assay reporting on the kinetics of extrinsic eukaryotic transcription termination by the Sen1 helicase and a reaction intermediate in which the Pol II transcription bubble appears half-rewound.

    • S. Wang
    • , Z. Han
    •  & T. R. Strick

  • Article
    | Open Access

    Upon photoactivation the Orange Carotenoid Protein (OCP) binds to the phycobilisome and prevents damage by thermally dissipating excess energy. Here authors use an Anti-Brownian ELectrokinetic trap to determine the photophysics of single OCP-quenched phycobilisomes and observe two distinct OCP-quenched states with either one or two OCPs bound.

    • Allison H. Squires
    • , Peter D. Dahlberg
    •  & W. E. Moerner

  • Article
    | Open Access

    Cryo-electron microscopy can determine the structure but not the nanomechanics of biological matter. Here the authors combine force spectroscopy in cryogenic conditions with computer simulations to characterize the properties of DNA simultaneously down to the sub-nm level.

    • Rémy Pawlak
    • , J. G. Vilhena
    •  & Ernst Meyer

  • Article
    | Open Access

    Analysis of single-molecule binding assays still requires substantial manual user intervention. Here, the authors present a pipeline for rapid, automated analysis of co-localization single-molecule spectroscopy images, with a modular user interface that can be adjusted to a range of experimental conditions.

    • Carlas S. Smith
    • , Karina Jouravleva
    •  & David Grunwald

  • Article
    | Open Access

    Ultrathin nanopore membranes have the potential for detecting topological variation in DNA. Here the authors use barcoded DNA to characterise the translocation profiles of DNA with single strand gaps.

    • Ke Liu
    • , Chao Pan
    •  & Aleksandra Radenovic

  • Article
    | Open Access

    Packaging of viral DNA depends on strong molecular motors that are powered by ATP hydrolysis. Here, the authors develop a single-molecule assay to monitor how nucleotide binding regulates motor-DNA interactions and reveal a generic mechanism that prevents exit of the whole DNA from the viral capsid during packaging.

    • Mariam Ordyan
    • , Istiaq Alam
    •  & Douglas E. Smith

  • Article
    | Open Access

    How DNA repair proteins locate their target sites on DNA is still a matter of debate. Here the authors characterize by single-molecule fluorescence imaging the modes of scanning adopted by bacterial endonuclease V as it moves along linear DNA tracks.

    • Arash Ahmadi
    • , Ida Rosnes
    •  & Alexander D. Rowe

  • Article
    | Open Access

    Zygotic genome activation (ZGA), the onset of transcription after initial quiescence, is a major developmental step in many species. Here authors use single molecule tracking in live developing zebrafish embryos to show that increased transcription factor binding to DNA at ZGA is due to a shrinking nucleus.

    • Matthias Reisser
    • , Anja Palmer
    •  & J. Christof M. Gebhardt

  • Article
    | Open Access

    Exocyst complex tethers vesicles to plasma membranes, but assembly mechanisms remain unclear. Here, the authors use Cas9 gene editing to tag exocyst components in epithelial cells, and find that exocyst subcomplexes are recruited to membranes independently, but are both needed for vesicle fusion.

    • Syed Mukhtar Ahmed
    • , Hisayo Nishida-Fukuda
    •  & Ian G. Macara

  • Article
    | Open Access

    The early steps of ribosome assembly occur co-transcriptionally on the nascent ribosomal RNA. Here the authors demonstrate an approach that allows simultaneous monitoring of transcription and ribosomal protein assembly at the single-molecule level in real time.

    • Olivier Duss
    • , Galina A. Stepanyuk
    •  & James R. Williamson

  • Article
    | Open Access

    The dynamics of biomolecules can occur over a wide range of time and length scales. Here the authors develop a high-speed AFM height spectroscopy method to directly detect the motion of unlabeled molecules at Angstrom spatial and microsecond temporal resolution.

    • George R. Heath
    •  & Simon Scheuring

  • Article
    | Open Access

    Intrinsically disordered proteins (IDPs) usually fold during binding to target proteins which involves the formation of a transient complex (TC). Here authors use single-molecule FRET to show that the lifetime of TC for IDP binding is very long due to the stabilization by non-native electrostatic interactions, which makes fast association possible.

    • Jae-Yeol Kim
    • , Fanjie Meng
    •  & Hoi Sung Chung

  • Article
    | Open Access

    Solid state nanopores are robust but the sizing can be variable, whereas protein nanopores are precisely sized but lack robustness. Here the authors cork a solid state nanopore with the DNA-translocating portal protein from the virus G20c to obtain a lipid-free hybrid nanopore that can sense various biopolymers.

    • Benjamin Cressiot
    • , Sandra J. Greive
    •  & Meni Wanunu

  • Article
    | Open Access

    Metal ions at the active site of an enzyme act as cofactors and their dynamic fluctuations might influence enzyme activity. Here authors use single-molecule FRET to study λ-exonuclease and find that metal-ion-coordination is correlated with enzymatic reaction-steps.

    • Wonseok Hwang
    • , Jungmin Yoo
    •  & Gwangrog Lee

  • Article
    | Open Access

    It was previously suggested that formation of RNA secondary structure tends to bring the 5′ and 3′ ends of RNA into close proximity. Here the authors use experimental and computational approaches to show that mRNAs and lncRNAs have an intrinsic propensity to fold into structures in which the 5′ end and 3′ end are ≤7 nm apart irrespective of length.

    • Wan-Jung C. Lai
    • , Mohammad Kayedkhordeh
    •  & Dmitri N. Ermolenko

  • Article
    | Open Access

    How G-quadruplexes (G4s) are resolved by helicases is still a matter of investigation. Here the authors provide mechanistic insight into G4s unwinding by presenting a crystal structure of resolved G4 DNA and the G4 binding domain of RecQ helicase from the bacterium Cronobacter sakazakii.

    • Andrew F. Voter
    • , Yupeng Qiu
    •  & James L. Keck

  • Article
    | Open Access

    Protein nanopores are emerging as sensors for a variety of biomolecules. Here the authors develop a nanopore based on the bacterial toxin ClyA, in conjunction with binding proteins for glucose and asparagine, to detect these biomolecules simultaneously from a variety of unprocessed, diluted body fluids.

    • Nicole Stéphanie Galenkamp
    • , Misha Soskine
    •  & Giovanni Maglia

  • Article
    | Open Access

    Cyclic nucleotide-gated (CNG) ion channels are non-selective cation channels key to signal transduction, but conformational changes associated with gating remained unknown. Here authors use high-speed atomic force microscopy to visualize SthK channels dynamics in response to cyclic nucleotides.

    • Arin Marchesi
    • , Xiaolong Gao
    •  & Simon Scheuring

  • Article
    | Open Access

    Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.

    • Francesco Simone Ruggeri
    • , Jerome Charmet
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    Omecamtiv mecarbil (OM) is a positive cardiac inotrope in clinical trials for the treatment of heart failure whose mechanism of action is incompletely understood. Here the authors show that OM inhibits myosin's working stroke and prolongs actomyosin attachment and propose a model that reconciles the OM-induced increase in cardiac performance in vivo with the inhibitory actions observed in vitro.

    • Michael S. Woody
    • , Michael J. Greenberg
    •  & E. Michael Ostap

  • Article
    | Open Access

    Processive chitinase is a linear molecular motor which moves on the surface of crystalline chitin. Here authors use single-molecule imaging, X-ray crystallography and simulations on chitinase A (SmChiA) and show that Brownian motion along the single chitin chain is rectified forward by substrate-assisted catalysis.

    • Akihiko Nakamura
    • , Kei-ichi Okazaki
    •  & Ryota Iino

  • Article
    | Open Access

    UPF1 is a highly processive helicase that plays an essential role in nonsense-mediated mRNA decay. Here the authors use single molecule binding assays to establish a functionally important relationship between helicase grip to nucleic acids, binding lifetime and the duration of translocation.

    • Joanne Kanaan
    • , Saurabh Raj
    •  & Hervé Le Hir

  • Article
    | Open Access

    The SNARE complex enables the fusion of synaptic vesicles with presynaptic membrane via a zippering process that is modulated by the protein complexin, though the precise mechanism remains unclear. Here, the authors used magnetic tweezers to show how complexin prepares a SNARE complex for fusion under mechanical tension.

    • Min Ju Shon
    • , Haesoo Kim
    •  & Tae-Young Yoon

  • Article
    | Open Access

    To date, the precise localisation of ligands and adhesion proteins are determined in two parallel characterization setups. Here, the authors report a self-assembled monolayer chemistry for indium tin oxide surfaces allowing single molecule localisation microscopy (SMLM) imaging of ligands and adhesion proteins in a single experiment.

    • Xun Lu
    • , Philip R. Nicovich
    •  & J. Justin Gooding

  • Article
    | Open Access

    The circadian clock proteins KaiA, KaiB, and KaiC reconstitute a circa-24 h oscillation of KaiC phosphorylation in vitro. Here the authors use high-speed atomic force microscopy to visualize in real time and quantify the dynamic interactions of KaiA with KaiC on the sub-second timescale to discover mechanisms of oscillatory resilience.

    • Tetsuya Mori
    • , Shogo Sugiyama
    •  & Toshio Ando

  • Article
    | Open Access

    Mechanical force can facilitate thermodynamically unfavourable reactions. Here, the authors found that a stretching force can promote the SN2 cleavage of a protein disulfide bond by weak nucleophilic thiols, and that removing this force reverses the reaction yielding the original disulfide bond.

    • Amy E. M. Beedle
    • , Marc Mora
    •  & Sergi Garcia-Manyes

  • Article
    | Open Access

    Large scale live cell screens often lack single-molecule resolution. Here the authors present an artificial intelligence-assisted TIRF microscope with automated cell searching and focusing, and use it for high-throughput single-molecule imaging of EGFR dynamics in response to various stimuli.

    • Masato Yasui
    • , Michio Hiroshima
    •  & Masahiro Ueda

  • Article
    | Open Access

    Transcription elongation by RNA polymerase (RNAP) is interspersed with sequence-dependent pausing which is difficult to study due to spatiotemporal limitations of available methods. Here authors use a high-resolution optical tweezers assay and find that pause sites modify the dynamics of nearly all RNAP molecules.

    • Ronen Gabizon
    • , Antony Lee
    •  & Carlos J. Bustamante

  • Article
    | Open Access

    Myosin-5B is an actin-based motor important for endosome recycling, but the molecular mechanism underlying its motility remains unknown. Here authors use single molecule imaging and high-speed laser tweezers to dissect the mechanoenzymatic properties of myosin-5B, which shows processive motility with peculiar mechanosensitivity.

    • Lucia Gardini
    • , Sarah M. Heissler
    •  & Marco Capitanio

  • Article
    | Open Access

    Cas12a is a RNA-guided DNA endonuclease whose detailed mechanisms of target searching and DNA cleavage remained unclear. Here authors use single-molecule fluorescence assays to show that Cas12a searches for their on-target site.

    • Yongmoon Jeon
    • , You Hee Choi
    •  & Sangsu Bae

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