Biophysical chemistry articles within Nature Communications

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  • Article
    | Open Access

    Short cationic peptides and nucleotides can form complex coacervates, but the influence of reduced multivalency on coacervate functionality was not investigated. Here, the authors report that coacervates formed from short polyions generate distinct pH microenvironments, accumulate RNA and preserve nucleic acid duplexes more efficiently than their longer counterparts.

    • Fatma Pir Cakmak
    • , Saehyun Choi
    •  & Christine D. Keating

  • Article
    | Open Access

    Almost all allosteric systems are large multi-domain proteins which complicates the investigation of the mechanism in atomistic detail. Here authors designed a small allosteric protein system using the photocontrollable PDZ3 domain, that allows controlling allostery between the binding and allosteric site in both directions.

    • Olga Bozovic
    • , Brankica Jankovic
    •  & Peter Hamm

  • Article
    | Open Access

    Membrane-less organelles or compartments are considered to be dynamic reaction centers for spatiotemporal control of diverse cellular processes. Here authors report quantitative measurements of changes in protein interactions for the proteins recruited into membrane-less compartments (termed client proteins) in living cells.

    • Daesun Song
    • , Yongsang Jo
    •  & Yongwon Jung

  • Article
    | Open Access

    Rhodopsin phosphodiesterase (Rh-PDE) hydrolyzes both cAMP and cGMP in a light-dependent manner. Structural and functional analyses of the Rh-PDE from Salpingoeca rosetta reveal unusual rhodopsin topology comprising 8 transmembrane helices (TMs) and suggest that TM0 plays a crucial role in the enzymatic photoactivity.

    • Tatsuya Ikuta
    • , Wataru Shihoya
    •  & Osamu Nureki

  • Article
    | Open Access

    The xrRNA1 RNA from ZIKA virus (ZIKV) forms a complex ring-like architecture and is known for its mechanical anisotropy, but the mechanism for its direction-dependent mechanical responses remain unclear. Here authors use a single-molecule nanopore sensing technique combined with molecular dynamics simulations and show that the anisotropy in ZIKV xrRNA1 depends on Mg2+ and the key tertiary interactions.

    • Xiaolin Niu
    • , Qiuhan Liu
    •  & Xianyang Fang

  • Article
    | Open Access

    Here, the authors present an approach that enhances the sensitivity of basic 2D biomolecular NMR experiments like NOESY and TOCSY, when carried out in polysaccharides, proteins and nucleic acids. This method combines principles associated to quantum Anti-Zeno Effects and advanced data acquisition methods based on Hadamard multiplexing.

    • Mihajlo Novakovic
    • , Ēriks Kupče
    •  & Lucio Frydman

  • Article
    | Open Access

    Multivalent ligand-receptor interactions enhance binding selectivity in biological systems, and may be exploited to design synthetic systems. Here the authors demonstrate a multivalent behavior where the ability to bind the target occurs when the receptor density is within a specific range.

    • Meng Liu
    • , Azzurra Apriceno
    •  & Stefano Angioletti-Uberti

  • Article
    | Open Access

    The design principles underlying biomolecular phase separation of membrane-less organelles remain poorly understood. Using model homopolymers, Fisher et al. show that the formation kinetics of coexisting liquid phases can be tuned by exploiting differences between arginine and lysine residues.

    • Rachel S. Fisher
    •  & Shana Elbaum-Garfinkle

  • Article
    | Open Access

    SARS-CoV-2 spike protein binds host ACE2 for virus entry. Here, the authors determine kinetic and thermodynamic properties of this interaction using atomic force microscopy, develop peptides that inhibit binding and suggest existence of additional attachment factors.

    • Jinsung Yang
    • , Simon J. L. Petitjean
    •  & David Alsteens

  • Article
    | Open Access

    The change from low-spin hexacoordinated to high-spin pentacoordinated domed form in heam upon ligand detachment and the reverse process underlie the respiratory function. The authors, using femtosecond time-resolved X-ray emission spectroscopy, capture the transient states connecting the two forms in myoglobin-NO upon NO photoinduced detachment.

    • Dominik Kinschel
    • , Camila Bacellar
    •  & Majed Chergui

  • Article
    | Open Access

    G-quadruplex (G4) forming sequences are highly enriched in the human genome and function as important regulators of diverse range of biological processes. Here the authors show that while G4 structures on template strand block transcription, folding on the non-template strand enhances transcription by means of successive R-loop formation.

    • Chun-Ying Lee
    • , Christina McNerney
    •  & Sua Myong

  • 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

    ESCRT-III proteins assemble into ubiquitous membrane-remodeling polymers during many cellular processes. Here, the authors use cryo-ET, cryo-EM and mathematical modeling to reveal how the shape of the helical membrane tube arises from the assembly of two distinct bundles of helical filaments.

    • Joachim Moser von Filseck
    • , Luca Barberi
    •  & Aurélien Roux

  • Article
    | Open Access

    Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. Here, the authors use single-molecule assays to examine the mechanism of action of CHD4 remodeller, and provide evidence that CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation.

    • Yichen Zhong
    • , Bishnu P. Paudel
    •  & Joel P. Mackay

  • Article
    | Open Access

    Proper membrane physiology requires maintenance of a narrow range of physicochemical properties, which must be buffered from external perturbations. Here, authors report lipidomic remodeling to preserve membrane physical properties upon exogenous polyunsaturated fatty acids exposure.

    • Kandice R. Levental
    • , Eric Malmberg
    •  & Ilya Levental

  • Article
    | Open Access

    Bilaterian mitochondria-encoded tRNA genes accumulate mutations at higher rates than their cytoplasmic tRNA counterparts, resulting in idiosyncratic structures. Here the authors suggest an evolutionary basis for the observed mutational freedom of mitochondrial (mt) tRNAs and reveal the associated co-adaptive structural and functional changes in mt aminoacyl-tRNA synthetases.

    • Bernhard Kuhle
    • , Joseph Chihade
    •  & Paul Schimmel

  • Article
    | Open Access

    To carry out their function, transcription factors must efficiently recognize specific DNA sequence targets, a complex problem in the context of eukaryotic chromatin. Here the authors use single-molecule biophysical experiments, statistical mechanical theory and bioinformatics analyses to conclude that interactions with non-target sequences near promoters serve to increase overall affinity and targeting efficiency.

    • Milagros Castellanos
    • , Nivin Mothi
    •  & Victor Muñoz

  • Article
    | Open Access

    Many RNA systems possess highly ordered 3-D structures that are essential to their function. Here the authors demonstrate that the long non-coding RNA Braveheart possesses a flexible but defined 3-D structure which is remodeled upon binding the protein CNBP.

    • Doo Nam Kim
    • , Bernhard C. Thiel
    •  & Karissa Y. Sanbonmatsu

  • Article
    | Open Access

    Mobile group II introns function as ribozymes to splice and reinsert themselves into DNA, thereby colonizing new genomic regions. Here the authors use single-molecule FRET and molecular dynamics simulations to reveal a structural link between metal ion induced kinetic heterogeneity and the sugar puckers at the exon-intron binding interface.

    • Fabio D. Steffen
    • , Mokrane Khier
    •  & Roland K. O. Sigel

  • Article
    | Open Access

    Liquid-liquid phase separation (LLPS) of intrinsically disordered proteins plays an important part in the formation of extracellular biological materials. Here, the authors show that repeats of the peptide motif GHGLY are necessary for the LLPS of pH-responsive histidine-rich squid beak proteins.

    • Bartosz Gabryelczyk
    • , Hao Cai
    •  & Ali Miserez

  • Article
    | Open Access

    Nanopores have a wide range of applications in the field of sensing. Here the authors report on synthetic nanopores made of DNA and designed for the transit of folded proteins across membranes to allow for biosensing.

    • Tim Diederichs
    • , Genevieve Pugh
    •  & Stefan Howorka

  • Article
    | Open Access

    Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here, the authors prepared a metallo-DNA duplex including two C-Hg(II)-T base pairs separated by six normal Watson-Crick base pairs and investigated its solution structure and dynamics using NMR spectroscopy.

    • Olivia P. Schmidt
    • , Simon Jurt
    •  & Nathan W. Luedtke

  • Article
    | Open Access

    Activatable fluorophores are of interest for a wide range of applications but the need for caging groups complicates their development and application. Here, the authors report on a photoactivatable silicon rhodamine derivative and its application in live cell imaging and single-particle tracking.

    • Michelle S. Frei
    • , Philipp Hoess
    •  & Kai Johnsson

  • Article
    | Open Access

    Understanding the fusion of nanocarriers with cell membranes is important to the design of effective drug delivery methods. Here, the authors report on a study into the fusion of cubosomes with model cell membranes underflow conditions and report on the binding kinetics.

    • Brendan P. Dyett
    • , Haitao Yu
    •  & Charlotte E. Conn

  • Article
    | Open Access

    Argonaute protein is loaded with small RNA and scans long stretch of sequences to find complementary target sites. Here, using single-molecule FRET and kinetic modelling, the authors showed that prokaryotic Argonaute protein binds target DNA loosely and slides along the DNA during target search.

    • Tao Ju Cui
    • , Misha Klein
    •  & Chirlmin Joo

  • Article
    | Open Access

    Many animals use the Earth’s magnetic field for orientation, yet the underlying principles are poorly understood. The authors show that a molecular triad acts as a chemical compass in magnetic fields of similar magnitude to that of the Earth, supporting the hypothesis that photo-initiated quantum processes underlie bird magnetoreception.

    • Christian Kerpal
    • , Sabine Richert
    •  & Christiane R. Timmel

  • Article
    | Open Access

    The ability to encapsulate living cells could lead to many applications. Here, the authors present a flexible method to graft DNA polymers onto bacteria, yeast and mammalian cells, polymerize them into DNA cocoons and use these to manipulate and select cells based on the encoded polymer sequences on DNA cocoons.

    • Tao Gao
    • , Tianshu Chen
    •  & Genxi Li

  • Article
    | Open Access

    The SLC26 family of transporters maintains anion equilibria in all kingdoms of life. Here, the authors resolve the structure of an SLC26 dimer embedded in a lipid membrane and characterize it by PELDOR/DEER distance measurements, biochemical studies with MD simulations and spin-label ensemble refinement.

    • Yung-Ning Chang
    • , Eva A. Jaumann
    •  & Eric R. Geertsma

  • Article
    | Open Access

    Polyglutamine (polyQ) tracts are low-complexity regions and their expansion is linked to certain neurodegenerative diseases. Here the authors combine experimental and computational approaches to find that the length of the androgen receptor polyQ tract correlates with its helicity and show that the polyQ helical structure is stabilized by hydrogen bonds between the Gln side chains and main chain carbonyl groups.

    • Albert Escobedo
    • , Busra Topal
    •  & Xavier Salvatella

  • Article
    | Open Access

    The serotonin transporter (SERT) is responsible for re-uptake of serotonin into the presynaptic neuron and plays a key role in synaptic transmission. Here, the authors use hydrogen-deuterium exchange mass spectrometry to probe the conformational dynamics of human SERT in the absence and presence of known substrates and targeted drugs.

    • Ingvar R. Möller
    • , Marika Slivacka
    •  & Kasper D. Rand

  • Article
    | Open Access

    Super-resolution microscopy with spontaneously blinking dyes is dependent on pH and polarity of the medium. Here the authors introduce a photoactivatable fluxional fluorophore for live cell imaging that allows control over the fraction of spontaneously blinking molecules independently of medium properties.

    • Elias A. Halabi
    • , Dorothea Pinotsi
    •  & Pablo Rivera-Fuentes

  • Article
    | Open Access

    Chromatophores in cephalopod skin are known for fast changes in coloration due to light-scattering pigment granules. Here, authors demonstrate structural coloration facilitated by reflectin in sheath cells and offer insights into the interplay between structural and pigmentary coloration elements.

    • Thomas L. Williams
    • , Stephen L. Senft
    •  & Leila F. Deravi

  • Article
    | Open Access

    Designing interfaces that can induce protein-protein interactions is a challenging problem. Here the authors show that a five amino acid sequence known to mediate domain swapping in cystatins can drive oligomerization when grafted onto functionally and structurally unrelated host proteins, providing a simple approach to the design of protein assemblies.

    • Neha Nandwani
    • , Parag Surana
    •  & Shachi Gosavi

  • 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

    Radiation-induced low-energy electrons in solution are implicated in DNA damage, but their relaxation dynamics are not well understood. Here the authors observe how quasi-free electrons dissociate glycosidic bonds via an excited nucleoside anion radical, whereas solvated electrons reside on the nucleoside as a relatively stable anion radical.

    • Jun Ma
    • , Anil Kumar
    •  & Mehran Mostafavi

  • Article
    | Open Access

    How intrinsically disordered proteins (IDPs) undergo a coupled folding and binding reaction with their molecular targets remains to be understood. Here authors use single-molecule FRET to assess the contribution of cis/trans isomerization of peptidyl-prolyl bonds in regulating IDP interactions.

    • Franziska Zosel
    • , Davide Mercadante
    •  & Benjamin Schuler

  • 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

    The potent antibacterial compound albicidin is synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. Here the authors employ a multidisciplinary approach and provide structural and mechanistic insights into how the drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca.

    • Lida Rostock
    • , Ronja Driller
    •  & Roderich D. Süssmuth

  • Article
    | Open Access

    In Escherichia coli, outer membrane protein (OMP) cluster and form islands, but the origin and behaviour of those clusters remains poorly understood. Here authors use coarse grained molecular dynamics simulation and show that their mesoscale simulations recapitulate the restricted diffusion characteristics of OMPs.

    • Matthieu Chavent
    • , Anna L. Duncan
    •  & Mark S. P. Sansom

  • 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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