Biological fluorescence articles within Nature Communications

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  • Article
    | Open Access

    Here, the authors use small angle neutron scattering and coarse-grained molecular dynamics simulations to demonstrate that condensates based on the granular components of nucleoli are network fluids.

    • Furqan Dar
    • , Samuel R. Cohen
    •  & Rohit V. Pappu

  • Article
    | Open Access

    Trait correlations impact evolvability as selection on one trait can influence others. Here, the authors examine trait correlation in two proteins, a fluorescent protein & an antibiotic resistance enzyme, observing rapid evolution of trait correlations through changes in the biophysical properties of these proteins.

    • Pouria Dasmeh
    • , Jia Zheng
    •  & Andreas Wagner

  • Article
    | Open Access

    The wide variety of cellular processes involving biomolecular condensation makes their quantification a challenging task. Here, the authors present an integrated platform based on single-photon microscopy to study complex biomolecular processes.

    • Eleonora Perego
    • , Sabrina Zappone
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    Multicolor imaging employing genetically-encodable fluorescent proteins permits spatiotemporal live cell imaging of multiple cues. Here, authors use multicolor lifetime imaging to visualize quadruple-labelled human immunodeficiency viruses within cellular contexts.

    • Tobias Starling
    • , Irene Carlon-Andres
    •  & Sergi Padilla-Parra

  • Article
    | Open Access

    Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here the authors design spirocyclic rhodamine probes that enable a fluorescent light-up aptamer system suitable for visualizing RNAs in live or fixed cells with two different super-resolution microscopy modalities SMLM and STED.

    • Daniel Englert
    • , Eva-Maria Burger
    •  & Murat Sunbul

  • Article
    | Open Access

    The recently discovered aptamer Beetroot is a homodimeric RNA that binds and activates DFAME, a conditional, red-shifted fluorophore derived from GFP. Here the authors determine the Beetroot-DFAME co-crystal structure, which is distinctively different from that of similar RNA aptamer Corn.

    • Luiz F. M. Passalacqua
    • , Mary R. Starich
    •  & Adrian R. Ferré-D’Amaré

  • Article
    | Open Access

    Glycine receptors are channel receptors mediating signal transduction between neurons that transit between resting and open states upon neurotransmitter binding. Here, the authors illuminate a progressive transition of opening by combining voltage-clamp fluorometry and molecular dynamics.

    • Sophie Shi
    • , Solène N. Lefebvre
    •  & Pierre-Jean Corringer

  • Article
    | Open Access

    Single-molecule localization microscopy relies on stochastic blinking events, treated as independent events without assignment to a particular emitter. Here, BaGoL takes low precision localizations generated from multiple emitter blinkings during DNAPAINT and dSTORM and finds the underlying emitter positions with high precision.

    • Mohamadreza Fazel
    • , Michael J. Wester
    •  & Keith A. Lidke

  • 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

    It is important to understand the enzymatic degradation of wood biomass by lytic polysaccharide monooxygenase, however, disagreements about the co-substrate exist. Here, the authors use piezo-controlled hydrogen peroxide micro-sensors to demonstrate that even low levels of hydrogen peroxide support the enzymatic degradation of wood cell walls.

    • Hucheng Chang
    • , Neus Gacias Amengual
    •  & Roland Ludwig

  • Article
    | Open Access

    FtsN promotes the inward synthesis of septal peptidoglycan (sPG) through the FtsWI complex during bacterial cell division. Here, Lyu et al. apply single-molecule microscopy on E. coli to show that FtsN proteins (I) move processively at a speed similar to that of FtsWI molecules. (II) can be divided into two populations based on their speeds, and (III) their movement is driven exclusively by peptidoglycan synthesis

    • Zhixin Lyu
    • , Atsushi Yahashiri
    •  & Jie Xiao

  • Article
    | Open Access

    The authors present an in-depth investigation of excited state dynamics and molecular mechanism of the voltage sensing in microbial rhodopsins. Using a combination of spectroscopic investigations and molecular dynamics simulations, the study proposes the voltage-modulated deprotonation of the chromophore as the key event in the voltage sensing. Thus, molecular constraints that may further improve the fluorescence quantum yield and the voltage sensitivity are presented.

    • Arita Silapetere
    • , Songhwan Hwang
    •  & Peter Hegemann

  • Article
    | Open Access

    The Ca2+ modulated pulsatile glucagon and insulin secretions by pancreatic α and β cells are critical in glucose homeostasis. Here the authors show that the Ca2+ oscillations of α and β cells are phase-locked, and that the oscillation pattern is tuned by paracrine interactions between α and β cells.

    • Huixia Ren
    • , Yanjun Li
    •  & Chao Tang

  • Article
    | Open Access

    Some cyanobacteria acclimate to far-red light by integrating chlorophyll f into their photosystems. Additional chlorophylls typically slow down charge separation but here the authors show that charge separation in chlorophyll-f-containing Photosystem II is faster in the presence of red-shifted allophycocyanin antennas.

    • Vincenzo Mascoli
    • , Ahmad Farhan Bhatti
    •  & Roberta Croce

  • Article
    | Open Access

    Single-molecule localisation microscopy does not give orientation information. Here the authors combine Stochastic Optical Reconstruction Microscopy (STORM) with single molecule orientation and wobbling measurements using four-polarisation image splitting, 4polar-STORM.

    • Caio Vaz Rimoli
    • , Cesar Augusto Valades-Cruz
    •  & Sophie Brasselet

  • Article
    | Open Access

    The FRET efficiency usually predominantly depends on the proximity of donor and acceptor. Here the authors report an anisotropy-based mode of FRET detection, FRET-induced Angular Displacement Evaluation via Dim donor (FADED), to allow quantification of the relative angle between donor and acceptor.

    • Danai Laskaratou
    • , Guillermo Solís Fernández
    •  & Hideaki Mizuno

  • Article
    | Open Access

    53BP1 is a crucial factor involved in double strand break repair which blocks DNA end resection affecting DNA repair pathway choice. Here the authors reveal by live cell nuclear architecture analysis the spatiotemporal dynamics of 53BP1 oligomerization during a DSB DNA damage response.

    • Jieqiong Lou
    • , David G. Priest
    •  & Elizabeth Hinde

  • Article
    | Open Access

    To overcome the limitation of FRET data being too sparse to cover all structural details, FRET experiments need to be carefully designed and complemented with simulations. Here the authors present a toolkit for automated design of FRET experiments, which determines how many and which FRET pairs should be used to maximize the accuracy, and for FRET-assisted structural modeling and refinement at the atomistic level.

    • Mykola Dimura
    • , Thomas-Otavio Peulen
    •  & Holger Gohlke

  • Article
    | Open Access

    Proton-linked monocarboxylate transporters (MCTs) facilitate monocarboxylate efflux in glycolytically active cells and regulate transport down in glycolytically inactive cells. Here authors show a steep dependence of human MCT2 activity on substrate concentration and show the structural basis of cooperative transport.

    • Bo Zhang
    • , Qiuheng Jin
    •  & Sheng Ye

  • Article
    | Open Access

    Fluorogenic RNA aptamers have been used for RNA imaging, but folding and fluorescence stability often limited their use in high resolution applications. Here the authors present an array of stably folding Mango II aptamers for imaging of coding and non-coding RNAs at single-molecule resolution, in both live and fixed cells.

    • Adam D. Cawte
    • , Peter J. Unrau
    •  & David S. Rueda

  • Article
    | Open Access

    T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.

    • Hugo Sanabria
    • , Dmitro Rodnin
    •  & Claus A. M. Seidel

  • 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

    The authors use accelerated protons on photosensitizers (PS, conventionally excited by light), to generate fluorescence and singlet oxygen which can enhance the efficacy of proton therapy. A pilot study on glioblastoma cells confirms differential cell death upon irradiation in the presence of PS.

    • M. Grigalavicius
    • , M. Mastrangelopoulou
    •  & T. A. Theodossiou

  • Article
    | Open Access

    Fluorescence correlation spectroscopy is widely used for in vivo and in vitro applications, yet extracting information from experiments still requires long acquisition times. Here, the authors exploit Bayesian non-parametrics to directly analyze the output of confocal fluorescence experiments thereby probing physical processes on much faster timescales.

    • Sina Jazani
    • , Ioannis Sgouralis
    •  & Steve Pressé

  • 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 FtsZ protein assembles into a structure known as ‘Z-ring’ at midcell for bacterial cell division. Here, Söderström et al. show that Z-ring assembly and dynamics in E. coli cells with unnatural shapes, such as squares and hearts, are generally similar to those observed in cells with normal shape.

    • Bill Söderström
    • , Alexander Badrutdinov
    •  & Ulf Skoglund

  • Article
    | Open Access

    Biologically relevant weak and transient interdomain interactions within proteins are difficult to analyze. Here, the authors combine multiscale molecular dynamics simulations and high-precision FRET experiments to characterize interactions between the tandem PDZ domains of PSD-95, revealing previously hidden conformational states.

    • Inna S. Yanez Orozco
    • , Frank A. Mindlin
    •  & Hugo Sanabria

  • Article
    | Open Access

    Outer membrane proteins (OMPs) in Gram-negative bacteria have restricted lateral mobility. Here, Rassam et al. show that the bacteriocin ColE9, via its interactions with OMPs, imposes this restricted mobility on the inner membrane proteins of the Tol-Pal complex.

    • Patrice Rassam
    • , Kathleen R. Long
    •  & Colin Kleanthous

  • Article
    | Open Access

    Myosin VI (MVI) is known to interact with RNA Polymerase II and to play non-cytoplasmic roles in cells. Here, the authors provide evidence that the transcription co-activator NDP52 regulates MVI binding to DNA and that MVI interacts with nuclear receptors to drive gene expression.

    • Natalia Fili
    • , Yukti Hari-Gupta
    •  & Christopher P. Toseland

  • Article
    | Open Access

    Natural silk fibers are produced using a simple and green approach compared to alternative synthetic methods. Here, the authors show a bioinspired approach to spin regenerated silk fibers using anisotropic liquid crystals and dry spinning, resulting in remarkably robust fibers.

    • Shengjie Ling
    • , Zhao Qin
    •  & Markus J. Buehler

  • Article
    | Open Access

    Measuring thein vivo stoichiometry of protein-protein interactions is challenging. Here the authors take a FRET-based approach, quantifying stoichiometry based on ratiometric comparison of donor and acceptor fluorescence, and apply their method to report on a Ca2+-induced switch in calmodulin binding to Ca2+ion channels.

    • Manu Ben-Johny
    • , Daniel N. Yue
    •  & David T. Yue

  • Article
    | Open Access

    In bacteria, CRISPR-Cas9 identifies and cleaves the target DNA with the assistance of a tracrRNA and a crRNA. Here the authors use single-molecule spectroscopy to investigate conformational changes and show that the tracrRNA keeps Cas9 in a functionally active form.

    • Youngbin Lim
    • , So Young Bak
    •  & Seong Keun Kim

  • Article
    | Open Access

    The actomyosin cytoskeleton consists of a contractile array but how it becomes organized is not clear. Here the authors reconstitute a controllable contractile system to show that force balances at boundaries determine contraction dynamics, and spatial anisotropy leads to self-organization or aligned contractile fibres.

    • Matthias Schuppler
    • , Felix C. Keber
    •  & Andreas R. Bausch

  • Article
    | Open Access

    Closure of epithelial gaps such as wounds is thought to involve contraction of an actomyosin ‘purse-string’. By creating non-adherent gaps to exclude contributions of adhesive protrusion, the authors find that large-scale tension, more than purse-string contraction, mediates closure.

    • Sri Ram Krishna Vedula
    • , Grégoire Peyret
    •  & Benoit Ladoux

  • Article
    | Open Access

    NAD and NADP play fundamentally different roles in cellular metabolism, and yet these pyridine nucleotides cannot be distinguished spectroscopically in living cells. Blacker et al.demonstrate that fluorescence lifetime imaging can be used to quantify NADPH/NADH balance in cultured cells and in the mammalian cochlea.

    • Thomas S. Blacker
    • , Zoe F. Mann
    •  & Michael R. Duchen

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