Biophysics articles within Nature Communications

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  • Article
    | Open Access

    Force-dependent formation of the talin-vinculin complex reinforces actin anchoring to focal adhesions, but how different talin-binding proteins respond to force is unclear. Here authors use an in vitro microscopy assay and show that the actomyosin force triggers the dissociation of RIAM from several talin domains.

    • Clémence Vigouroux
    • , Véronique Henriot
    •  & Christophe Le Clainche

  • Article
    | Open Access

    Phosphorylation of eIF4E binding proteins (4E-BPs) controls their folding and regulates cap-dependent translation. Here, the authors show that phosphorylation of the C-terminal disordered region stabilizes the non-cooperatively folded 4E-BP domain to an eIF4E binding-incompatible state to control translation.

    • Jennifer E. Dawson
    • , Alaji Bah
    •  & Julie D. Forman-Kay

  • Article
    | Open Access

    PIEZO2 is a critical component of the mechanism by which innocuous touch causes pain (tactile allodynia). Here, authors find that the dietary fatty acid margaric acid decreases PIEZO2 function in a dose-dependent manner and counteracts neuronal mechanical sensitization by a proalgesic agent.

    • Luis O. Romero
    • , Rebeca Caires
    •  & Valeria Vásquez

  • Article
    | Open Access

    The transition between conducting and non-conducting states of K+ channels has been explained by conformational changes at the intracellular entrance to the conduction pathway. Here authors demonstrate that control over K+ currents in Kir channels is not explained by the canonical pore-gating model, as conduction is not impaired by a constricted inner helix bundle.

    • Katrina A. Black
    • , Sitong He
    •  & Jacqueline M. Gulbis

  • Article
    | Open Access

    Symmetric or asymmetric positioning of intracellular structures such as the nucleus and mitotic spindle steers various biological processes. Here authors use an in vitro model and show that a tug-of-war between centripetal actomyosin waves and percolation of bulk actomyosin network direct the positioning.

    • Ryota Sakamoto
    • , Masatoshi Tanabe
    •  & Makito Miyazaki

  • Article
    | Open Access

    Formation of amyloid-beta (Aβ) oligomer pores in the membrane of neurons has been proposed to explain neurotoxicity in Alzheimer´s disease. Here authors present the 3D- structure of an Aβ oligomer formed in a membrane mimicking environment and observe that Aβ tetramers and octamers inserted into lipid bilayers as well-defined pores.

    • Sonia Ciudad
    • , Eduard Puig
    •  & Natàlia Carulla

  • Article
    | Open Access

    Budding yeast cell polarization is known to self-assemble, but it is still not clear what controls the size of the resulting septin ring. Here the authors show that the septin ring diameter is set by cell volume, ensuring that larger cells have larger rings.

    • I. V. Kukhtevich
    • , N. Lohrberg
    •  & K. M. Schmoller

  • Article
    | Open Access

    Explicit molecular modelling of biological membrane systems is computationally expensive due to the large number of solvent particles and slow membrane kinetics. Here authors present a framework for integrating coarse-grained membrane models with continuum-based hydrodynamics which facilitates efficient simulation of large biomembrane systems.

    • Mohsen Sadeghi
    •  & Frank Noé

  • 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

    Multi-subunit Cullin (CUL)-RING ligases (CRL) form the largest family of E3 ligases and are composed of a substrate receptor, a CUL, and a RING-box (RBX) protein. Here, the authors use cryo-EM and HDX-MS to characterise the ASB9 CUL-RING E3 ligase and present the structure of ASB9-ELOB/C bound to the substrate creatine kinase and the full-length CUL5 structure in complex with RBX2, and they propose a revised allosteric mechanism for CUL-E3 ligase function.

    • Ryan J. Lumpkin
    • , Richard W. Baker
    •  & Elizabeth A. Komives

  • 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

    In Parkinson’s disease (PD) the monomeric protein alpha-synuclein (aSyn) misfolds and aggregates into insoluble fibrils. Here the authors use NMR measurements and hydrogen–deuterium exchange mass spectrometry and find that the more solvent exposed the N-terminus of aSyn is, the more aggregation prone its conformation becomes, and further show how PD mutations and post translational modifications influence the extent of the N-terminus solvent exposure.

    • Amberley D. Stephens
    • , Maria Zacharopoulou
    •  & Gabriele S. Kaminski Schierle

  • Article
    | Open Access

    Small molecule polyamines participate in diverse aspects of cell growth and differentiation and are known to regulate ion channel gating. Here authors reveal that cellular polyamines control nicotinic acetylcholine receptor (nAChR) biogenesis, and either catabolic degradation or inhibition of polyamine production augments nAChR assembly.

    • Madhurima Dhara
    • , Jose A. Matta
    •  & David S. Bredt

  • Article
    | Open Access

    DmpR is a bacterial enhancer binding protein from the AAA+ family of ATPases that binds aromatic compounds and controls the transcription of genes involved in the degradation of toxic pollutants. Here, the authors present the crystal structure of phenol-bound DmpR, which forms a tetramer and discuss its signal transduction mechanism.

    • Kwang-Hyun Park
    • , Sungchul Kim
    •  & Eui-Jeon Woo

  • Article
    | Open Access

    ESCRT-III complexes assemble in vivo inside membrane structures with a negative Gaussian curvature, but how membrane shape influences ESCRT-III polymerization remains unclear. Here authors use structural and biophysical methods to show how human ESCRT-III polymers assemble on positively curved membranes and induce helical membrane tube formation.

    • Aurélie Bertin
    • , Nicola de Franceschi
    •  & Patricia Bassereau

  • Article
    | Open Access

    F1Fo ATP synthase consists of two coupled rotary molecular motors: the soluble ATPase F1 and the transmembrane Fo. Here, the authors present cryo-EM structures of E. coli ATP synthase in four discrete rotational sub-states at 3.1-3.4 Å resolution and observe a rotary sub-step of the Fo motor cring that reveals the mechanism of elastic coupling between the two rotary motors, which is essential for effective ATP synthesis.

    • Meghna Sobti
    • , James L. Walshe
    •  & Alastair G. Stewart

  • 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

    There is a need to further improve the automation of cryo-EM sample preparation to make it more easily accessible for non-specialists, reduce sample waste and increase reproducibility. Here, the authors present VitroJet, a single device, where sub-nl volumes of samples are deposited by pin printing thus eliminating the need for sample blotting, which is followed by jet vitrification, and they show that high-resolution structures can be obtained using four standard proteins.

    • Raimond B. G. Ravelli
    • , Frank J. T. Nijpels
    •  & Peter J. Peters

  • Article
    | Open Access

    The α-cardiac actin M305L hypertrophic cardiomyopathy-causing mutation is located near residues that help confine tropomyosin to an inhibitory position along thin filaments. Here the authors assessed M305L actin in vivo, in vitro, and in silico to characterize emergent pathological properties and define the mechanistic basis of disease.

    • Meera C. Viswanathan
    • , William Schmidt
    •  & Anthony Cammarato

  • 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

    Cytosolic ion gradients in growing pollen tubes are thought to be required for polar growth. Here the authors show that the Arabidopsis plasma membrane H+ ATPases, AHA6, AHA8, and AHA9, maintain tip-to-shank proton gradients, oscillations in cytosolic pH and actin organization to enable pollen tube elongation.

    • Robert D. Hoffmann
    • , Maria Teresa Portes
    •  & Michael Palmgren

  • Article
    | Open Access

    Neutrophils mobilize rapidly and travel through the vasculature and microcirculation en masse in response to inflammatory stimuli. Here the authors use a microfluidic device and intravital microscopy to show neutrophils move through tissues in a highly ordered pattern, taking turns to file into alternate branches at bifurcations.

    • Xiao Wang
    • , Mokarram Hossain
    •  & Daniel Irimia

  • Article
    | Open Access

    Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.

    • Weria Pezeshkian
    • , Melanie König
    •  & Siewert J. Marrink

  • Article
    | Open Access

    Auxin-mediated recruitment of AUX/IAAs by the F-box protein TIR1 prompts rapid AUX/IAA ubiquitylation and degradation. By resolving auxin receptor topology, the authors show that intrinsically disordered regions near the degrons of two Aux/IAA proteins reinforce complex assembly and position Aux/IAAs for ubiquitylation.

    • Michael Niemeyer
    • , Elena Moreno Castillo
    •  & Luz Irina A. Calderón Villalobos

  • Article
    | Open Access

    The evolutionarily conserved complex, the Par proteins, regulates cell polarity. Here, the authors show that in Drosophila neuroblasts, the Par complex exhibits liquid–liquid phase separation dependent on the cell cycle.

    • Ziheng Liu
    • , Ying Yang
    •  & Wenyu Wen

  • Article
    | Open Access

    The existence, nature and biological relevance of mechanoradicals in proteins are unknown. Here authors show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species and suggest that collagen I evolved as a radical sponge against mechano-oxidative damage.

    • Christopher Zapp
    • , Agnieszka Obarska-Kosinska
    •  & Frauke Gräter

  • Article
    | Open Access

    The contribution of central and peripheral channels of nuclear pores to transport of transmembrane proteins is unclear. Here the authors show that most inner nuclear membrane proteins use only peripheral channels, but some extend nuclear localization signals into the central channel for directed nuclear transport.

    • Krishna C. Mudumbi
    • , Rafal Czapiewski
    •  & Weidong Yang

  • Article
    | Open Access

    Potassium (K+) channels, such as MthK, are essentional for many biological processes, but how lipid-protein interactions regulate ion permeation of K+ channels remained unclear. Here authors conducted molecular dynamics simulations of MthK and observed different ion permeation rates of MthK in membranes with different properties.

    • Ruo-Xu Gu
    •  & Bert L. de Groot

  • Article
    | Open Access

    Dpr (Defective proboscis extension response) and DIP (Dpr Interacting Proteins) are immunoglobulin-like cell-cell adhesion proteins that form highly specific pairwise interactions, which control synaptic connectivity during Drosophila development. Here, the authors combine a computational approach with binding affinity measurements and find that DIP/Dpr binding specificity is controlled by negative constraints that interfere with non-cognate binding.

    • Alina P. Sergeeva
    • , Phinikoula S. Katsamba
    •  & Barry Honig

  • Article
    | Open Access

    The Na+-pumping KR2 rhodopsin from Krokinobacter eikastus is a light-driven non-proton cation pump whose mechanism of pumping remains to be understood. Here authors solved crystal structures of the O-intermediate state of the pentameric form of KR2 and its D116N and H30A mutants, which sheds light on the mechanism of non-proton cation light-driven pumping.

    • Kirill Kovalev
    • , Roman Astashkin
    •  & Valentin Gordeliy

  • Article
    | Open Access

    The mechanism of PARP1-dependent poly-ADP-ribosylation in response to DNA damage is still under debate. Here, the authors use ATR-FTIR spectroscopy to provide time-resolved insights into the molecular details of this process under near physiological conditions.

    • Annika Krüger
    • , Alexander Bürkle
    •  & Aswin Mangerich

  • Article
    | Open Access

    Precise patterning of lipid-stabilised aqueous droplets is a key challenge in building synthetic tissue designs. Here, the authors show how the interactions between pairs of droplets direct the packing of droplets within 3D-printed networks, enabling the formation of synthetic tissues with high-resolution features.

    • Alessandro Alcinesio
    • , Oliver J. Meacock
    •  & Hagan Bayley

  • Article
    | Open Access

    Mass photometry is a label-free optical approach capable of detecting, imaging and accurately measuring the mass of single biomolecules in solution. Here, the authors demonstrate the potential of mass photometry for quantitatively characterizing sample heterogeneity of purified protein complexes with implications for structural studies specifically and in vitro studies more generally.

    • Adar Sonn-Segev
    • , Katarina Belacic
    •  & Philipp Kukura

  • Article
    | Open Access

    Lipoprotein Lpp provides a covalent crosslink between the outer membrane and the peptidoglycan in E. coli. Here, the authors use atomic force microscopy to show that Lpp contributes to cell envelope stiffness by covalently connecting the two layers and by controlling the width of the periplasmic space.

    • Marion Mathelié-Guinlet
    • , Abir T. Asmar
    •  & Yves F. Dufrêne

  • Article
    | Open Access

    Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients and consist of an integral membrane unit, the S-component, which confers substrate specificity. Here, authors present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter.

    • Ignacio Faustino
    • , Haleh Abdizadeh
    •  & Siewert J. Marrink

  • Article
    | Open Access

    The phase separation of two species of associating polymers is suppressed by a magic-number effect for certain combinations of the numbers of binding sites. Here the authors use lattice simulations and analytical calculations to show that this magic-number effect can be greatly enhanced if one component has a rigid shape.

    • Bin Xu
    • , Guanhua He
    •  & Ned S. Wingreen

  • Article
    | Open Access

    Acyl-acyl carrier protein reductase (AAR) and aldehyde deformylating oxygenase (ADO) are the two enzymes in a cyanobacterial alkane biosynthesis pathway that is of interest for biofuel production. Here the authors provide insights into the catalytic mechanisms of AAR and the coupling between the two enzymes by determining the crystal structures of AAR alone and three AAR–ADO complexes with various bound ligands.

    • Yu Gao
    • , Hongmei Zhang
    •  & Mei Li

  • 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

    SNX-BAR proteins are a family of PX and BAR domain-containing proteins with pivotal roles in trafficking processes. Here authors present the cryo-EM structure of the full-length fungal SNX-BAR Mvp1, which is an autoinhibited tetramer and provides critical insight into SNX-BAR function and regulation.

    • Dapeng Sun
    • , Natalia V. Varlakhanova
    •  & Marijn G. J. Ford

  • Article
    | Open Access

    Mfd recognizes stalled transcriptional complexes at sites of lesions and recruits the nucleotide excision repair proteins (UvrAB) to the site. Here the authors use live cell imaging in E. coli to demonstrate that coordinated ATP hydrolysis by UvrA and loading of UvrB on DNA facilitate the dissociation of Mfd from the handoff complex.

    • Han Ngoc Ho
    • , Antoine M. van Oijen
    •  & Harshad Ghodke

  • Article
    | Open Access

    How and which cell surface molecules are taken up by clathrin-independent endocytosis is an ongoing area of research. Here, the authors show that the tumor marker CD166 is a clathrin-independent cargo that is taken up by endophilin-A3 and galectin-8, which regulates cancer cell migration.

    • Henri-François Renard
    • , François Tyckaert
    •  & Pierre Morsomme

  • Article
    | Open Access

    Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are essential for rhythmic activity in the heart and brain. Here authors reverse the voltage dependence of HCN channels by mutating only two residues located at the interface between the voltage sensor and the pore domain.

    • Rosamary Ramentol
    • , Marta E. Perez
    •  & H. Peter Larsson

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