Molecular biophysics articles within Nature Communications

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  • Article
    | Open Access

    Amyloid fibrils of β2-microglobulin (β2m) can cause dialysis-related amyloidosis. Here, the authors show that a decrease in serum albumin levels in long-term dialysis deteriorates the inhibitory effects of serum milieux on supersaturation-limited amyloid formation of β2m, suggesting that macromolecular crowding protects the onset of amyloidosis.

    • Kichitaro Nakajima
    • , Keiichi Yamaguchi
    •  & Yuji Goto

  • 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

    Barley β-d-glucan glucohydrolase is a glycoside hydrolase family 3 (GH3) enzyme critical for growth and development. Here the authors carryout mutagenesis, structural analyses and multi-scale molecular dynamics to examine the binding and conformational behaviour of several β-d-glucosides during the substrate-product assisted catalysis that operates in GH3 hydrolases.

    • Sukanya Luang
    • , Xavier Fernández-Luengo
    •  & Maria Hrmova

  • Article
    | Open Access

    Cytoplasmic organization is a hallmark of living cells. Here, the authors make use of self-organizing cell extracts to examine how the emergence of large-scale organizations influences the microscopic diffusion of protein molecules in the cytoplasm.

    • William Y. C. Huang
    • , Xianrui Cheng
    •  & James E. Ferrell Jr

  • 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 Spns lipid transporters use ion gradients to drive substrate transport, including bioactive sphingolipids. Here, Dastvan et al. investigated how binding of protons powers the conformational changes that enable broad transport by a bacterial Spns.

    • Reza Dastvan
    • , Ali Rasouli
    •  & Emad Tajkhorshid

  • Article
    | Open Access

    Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment.

    • Lauren Ann Metskas
    • , Davi Ortega
    •  & Grant J. Jensen

  • Article
    | Open Access

    Sun et al. has studied the genetically encodable halotyrosines in proteins of the prokaryotic cell division machinery to elucidate the general role of halogenation in cellular lifespan and oxidative damage-induced diseases such as aging and cancer.

    • Huan Sun
    • , Haiyang Jia
    •  & Nediljko Budisa

  • Article
    | Open Access

    Ayala Mariscal et al have identified and characterized the interface of pathogenic Huntingtin and the molecular chaperone DNAJB1. Histidine-244 of the C-terminal domain of DNAJB1 is a key residues for binding to the poly-proline region of HTT. This binding site is specific for the interaction with Huntingtin.

    • S. M. Ayala Mariscal
    • , M. L. Pigazzini
    •  & J. Kirstein

  • Article
    | Open Access

    Born et al. describe interdomain allostery in the two domain peptidyl-prolyl isomerase Pin1 upon binding of two ligands. These ligands couple population shifts of extended and compact states to changes in the catalytic site of Pin1.

    • Alexandra Born
    • , Janne Soetbeer
    •  & Beat Vögeli

  • Article
    | Open Access

    Pulsed electron-electron double resonance spectroscopy (PELDOR/DEER) and single-molecule Förster resonance energy transfer spectroscopy (smFRET) are used to determine conformational changes and probe distances in biological macromolecules. Here the authors compare the methods on a large set of samples.

    • Martin F. Peter
    • , Christian Gebhardt
    •  & Gregor Hagelueken

  • Article
    | Open Access

    Mitochondrial Atm1 proteins play important roles in the maturation of certain cytosolic proteins. Here, the authors exploit cryo-EM to capture several structures of an Atm1. The findings shed new light on the molecular function of Atm1 transporters.

    • Ping Li
    • , Amber L. Hendricks
    •  & Pontus Gourdon

  • Article
    | Open Access

    Our understanding of how compartmentalisation and intercellular communication can tune enzyme reactions is still in its infancy. Here, the authors show that multi-enzyme reactions within semi-permeable compartments have distinct properties compared to reactions in buffer solution.

    • Adrian Zambrano
    • , Giorgio Fracasso
    •  & T-Y. Dora Tang

  • Article
    | Open Access

    Folded proteins are composed of secondary structures, α-helices and β-sheets, that are generally assumed to be stable. Here, the authors combine computational prediction with experimental validation to show that many sequence-diverse NusG protein domains switch completely from α-helix to β-sheet folds.

    • Lauren L. Porter
    • , Allen K. Kim
    •  & Marie-Paule Strub

  • Article
    | Open Access

    Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction.

    • Jeroen F. van Dyck
    • , Jonathan R. Burns
    •  & Frank Sobott

  • Article
    | Open Access

    Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.

    • Christin Pohl
    • , Gregory Effantin
    •  & Pernille Harris

  • Article
    | Open Access

    The mechanism of cold-activated TRPM8 channel activation remains unclear. Here, authors have determined structures of mouse TRPM8 in apo or ligand-bound states, providing insights into the activation of TRPM8 structures in different states.

    • Cheng Zhao
    • , Yuan Xie
    •  & Jiangtao Guo

  • Article
    | Open Access

    Protein kinase Cs (PKCs) define a central DAG-sensing node in intracellular phosphoinositide signaling pathways that regulate cell growth, differentiation, apoptosis, and motility. The structures of PKC C1 domain complexes with DAG and 4 agonists reveal the molecular basis of ligand recognition and capture.

    • Sachin S. Katti
    • , Inna V. Krieger
    •  & Tatyana I. Igumenova

  • Article
    | Open Access

    CryoEM of mitochondrial ATP synthase frozen during rotary catalysis reveals dramatic conformational changes in the peripheral stalk subcomplex, which enable the enzyme’s efficient synthesis of ATP.

    • Hui Guo
    •  & John L. Rubinstein

  • Article
    | Open Access

    Snf7 is the major component of the ESCRTIII membrane deformation system. Here, the authors used high-speed AFM to study Snf7 on nano-patterned and soft supports and show that loaded Snf7 spiral springs are curvature sensitive and deform membranes.

    • Nebojsa Jukic
    • , Alma P. Perrino
    •  & Simon Scheuring

  • Article
    | Open Access

    Tension stabilizes properly attached microtubules to kinetochores during chromosome segregation, and lack of tension leads to release. Here the authors show that tension directly suppresses Aurora B kinase mediated destabilization of reconstituted kinetochore-microtubule attachments, likely ensuring accurate chromosome segregation.

    • Anna K. de Regt
    • , Cordell J. Clark
    •  & Sue Biggins

  • 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

    Direct information on the dynamic interplay between membrane proteins and lipids is scarce. Here the authors report a detailed description of these close relationships by combining lipid nanodiscs and high-pressure NMR. They report the link between pressure and lipid compositions to the conformational landscape of the β-barrel OmpX and the α-helical BLT2 G Protein-Coupled Receptor in nanodiscs.

    • Alexandre Pozza
    • , François Giraud
    •  & Laurent J. Catoire

  • Article
    | Open Access

    Constriction of the selectivity filter is assumed to be a hallmark of C-type inactivation in K+ channels. Using different high-resolution methods, this study shows a distinct C-type inactivation mechanism in a KcsA mutant that emulates Kv-channels.

    • Ahmed Rohaim
    • , Bram J. A. Vermeulen
    •  & Markus Weingarth

  • Article
    | Open Access

    IP3 receptors are intracellular calcium channels involved in numerous signaling pathways. Here, the authors present the cryo-EM structures of type-3 IP3 receptors in multiple gating conformations, including the active state revealing the molecular mechanism of the receptor activation.

    • Emily A. Schmitz
    • , Hirohide Takahashi
    •  & Erkan Karakas

  • Article
    | Open Access

    Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.

    • Behrouz Eslami-Mossallam
    • , Misha Klein
    •  & Martin Depken

  • Article
    | Open Access

    Glutamate receptors comprise two obligate subunits and two subunits that confer distinct properties and functions to the specific tetramers, which also localize to distinct synaptic spines. Here, the authors use STimulated Emission Depletion nanoscopy (STED) to provide detailed insights into the spatial organization of glutamate receptor types.

    • Martin Hruska
    • , Rachel E. Cain
    •  & Matthew B. Dalva

  • Article
    | Open Access

    Allosteric regulation of proteins allows transduction and interconversion of biochemical signals. Here the authors construct an allosteric version of circular permutated NanoLuc that can be activated by a ligand; they use this to create biosensors to quantify their cognate ligand in human fluids.

    • Zhong Guo
    • , Rinky D. Parakra
    •  & Kirill Alexandrov

  • 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

    Ghrelin receptor regulates energy homeostasis through constitutive activity or by the ghrelin. Here the authors report two structures of ghrelin receptor bound to agonist and inverse agonist, providing insights into the mechanism of inverse agonism, which is of interest for specific ligand design.

    • Jiao Qin
    • , Ye Cai
    •  & Zhenhua Shao

  • Article
    | Open Access

    UVR8 is a plant photoreceptor that dissociates into monomers after sensing UV. Here, via ultrafast spectroscopy and computational calculations, the authors describe the dynamics of charge separation and charge neutralization in UVR8 and describe how these unzip interactions at the dimer interface.

    • Xiankun Li
    • , Zheyun Liu
    •  & Dongping Zhong

  • Article
    | Open Access

    Here, the authors present the cryo-EM structure of in vitro amyloid fibrils from recombinant SAA1.1 protein that were formed by seeding with fibrils purified from systemic AA amyloidosis tissue. This in vitro fibril structure resembles the structure of the ex vivo fibrils but differs from unseeded in vitro fibrils. These findings show that fibril morphologies can be propagated in vitro by seeding.

    • Thomas Heerde
    • , Matthies Rennegarbe
    •  & Marcus Fändrich

  • Article
    | Open Access

    Methods to quantitatively study liquid-liquid phase separation (LLPS) of proteins are lacking. Here the authors report Capillary flow experiments (Capflex) for the quantification of key LLPS parameters; they study Ddx4, the RP3 peptide and the aberrant liquid-to-solid phase transition of α-synuclein.

    • Emil G. P. Stender
    • , Soumik Ray
    •  & Alexander K. Buell

  • Article
    | Open Access

    Here, the authors perform a large-scale, high-throughput biochemical assay to determine the compatibility of over 300,000 domain recombination variants of the inward rectifier K+ channel Kir2.1. They derive rules for designing domain insertion variants that fold and traffic to the cell surface and conclude that the insertion of domains at protein termini is evolutionary favoured.

    • Willow Coyote-Maestas
    • , David Nedrud
    •  & Daniel Schmidt

  • Article
    | Open Access

    Revealing mechanisms of complex protein machines requires simultaneous exploration of multiple structural coordinates. Here the authors report two-colour fluorescence microscopy combined with photoinduced electron transfer probes to simultaneously detect two structural coordinates in single protein molecules.

    • Jonathan Schubert
    • , Andrea Schulze
    •  & Hannes Neuweiler

  • Article
    | Open Access

    Here the authors use nanovesicles, microfluidics and single-molecule methods to observe individual ligand binding events that stimulate activation of CNG ion channels. They find that binding is followed by a conformational change of either independent or weakly cooperative binding domains.

    • Vishal R. Patel
    • , Arturo M. Salinas
    •  & Marcel P. Goldschen-Ohm

  • Article
    | Open Access

    Living cells can harvest environmental energy to drive chemical processes. Here the authors design a minimal artificial system that achieves steady states at similar metabolic densities to microorganisms.

    • Andrea Testa
    • , Mirco Dindo
    •  & Paola Laurino

  • Article
    | Open Access

    The centriole exhibits an evolutionarily conserved 9-fold radial symmetry that stems from a cartwheel containing vertically stacked ring polymers that harbor 9 homodimers of the protein SAS-6. Here the authors show how dual properties inherent to surface-guided SAS-6 self-assembly possess spatial information that dictates correct scaffolding of centriole architecture.

    • Niccolò Banterle
    • , Adrian P. Nievergelt
    •  & Pierre Gönczy

  • Article
    | Open Access

    Molecular chaperones from the Hsp70 family can break up protein aggregates, including amyloids. Here, the authors utilize microfluidic diffusional sizing to assess the mechanism of α-synuclein (αS) disaggregation by the Hsc70–DnaJB1–Apg2 system, and show that single αS molecules are removed directly from the fibril ends.

    • Matthias M. Schneider
    • , Saurabh Gautam
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    How chromosomes, which are polymers with nearly billion base pairs, are packaged in the restricted nuclear volume is not well understood. Here, the authors combine polymer physics, nonequilibrium fluctuation theorem, and simulations to quantitatively predict the force-dependent velocity and step-size distribution of condensin, which facilitates the folding of chromosomes by loop extrusion.

    • Ryota Takaki
    • , Atreya Dey
    •  & D. Thirumalai

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