Biophysical chemistry articles within Nature Communications

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  • Article
    | Open Access

    Phase separation provides intracellular organisation via membraneless entities called biomolecular condensates. Here, the authors show that short, cationic peptide tags can drive biomolecular condensation of engineered proteins in E. coli through associative interactions with RNA.

    • Vivian Yeong
    • , Jou-wen Wang
    •  & Allie C. Obermeyer

  • Article
    | Open Access

    A central concept for characterising phase-separating systems is the phase diagram but generation of such diagrams for biomolecular systems is typically slow and low-throughput. Here the authors describe PhaseScan, a combinatorial droplet microfluidic platform for high-resolution acquisition of multidimensional biomolecular phase diagrams.

    • William E. Arter
    • , Runzhang Qi
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    To refold client proteins, HSP90 chaperone undergoes large structural rearrangements. Here the authors use NMR and molecular simulation and reveal structure and dynamics of a key functionally relevant metastable state of human HSP90α N-terminal domain.

    • Faustine Henot
    • , Elisa Rioual
    •  & Jerome Boisbouvier

  • Article
    | Open Access

    Targeting biomedically relevant protein-protein interactions is a long-lasting challenge in medicinal chemistry. Here, the authors develop a single α-helical peptide scaffold that can be tailored to target globular proteins of biomedical interest.

    • Albert Escobedo
    • , Jonathan Piccirillo
    •  & Xavier Salvatella

  • Article
    | Open Access

    The nuclear pore complex (NPC) barrier is a selective phase assembled from disordered but cohesive FG domains. The authors provide a thermodynamic description of an FG phase that is ultimately simplified and yet closely recapitulates NPC transport selectivity.

    • Sheung Chun Ng
    •  & Dirk Görlich

  • 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

    Water is an essential part of any biological system, yet many aspects of its role remain elusive. Here the authors show, in a paradigmatic ligand-protein system, that water modulates the ligand residence time in a complex and non-local way, with possible implications in drug design.

    • Narjes Ansari
    • , Valerio Rizzi
    •  & Michele Parrinello

  • Article
    | Open Access

    Here, the authors study ion transport mechanisms by introducing mutations to convert an electroneutral proton/potassium pump into a prototypical electrogenic sodium/potassium pump, explaining their selectivity and phosphorylation mechanisms.

    • Victoria C. Young
    • , Hanayo Nakanishi
    •  & Kazuhiro Abe

  • 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

    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

    Small solute carriers remain difficult to study by single particle cryo-EM. Here, the authors report the cryo-EM structure of human insulin-responsive glucose transporter GLUT4 (55 kDa) without rigid soluble domains or binders.

    • Yafei Yuan
    • , Fang Kong
    •  & Chuangye Yan

  • Article
    | Open Access

    Inhibiting alpha-synuclein self-assembly into amyloid structures, associated with Parkinson’s disease, is a potential therapeutic intervention. Here, the authors identify the domains/sequences that are essential for alpha-synuclein aggregation and test the activity of foldamer-based antagonists to identify potential therapeutic targets.

    • Jemil Ahmed
    • , Tessa C. Fitch
    •  & Sunil Kumar

  • Article
    | Open Access

    Phenolics are abundant in plant cuticles. Here, via transient absorption spectroscopy and quantum chemical calculations, the authors propose a model by which cuticle phenolics provide photoprotection due to ultrafast and non-radiative excited state deactivation combined with fluorescence emission.

    • Ana González Moreno
    • , Abel de Cózar
    •  & Antonio Heredia

  • Article
    | Open Access

    Nonphotochemical quenching (NPQ) protects photosynthetic complexes from damage due to excess light. Here the authors explore different conformations of the plant CP29 light harvesting complex, showing how protein tuning of carotenoid excitation energies and carotenoid-chlorophyll interactions account for NPQ.

    • Edoardo Cignoni
    • , Margherita Lapillo
    •  & Benedetta Mennucci

  • Article
    | Open Access

    AL amyloidosis is caused by the accumulation of overproduced light chain (LC) fragments as fibrils in patient organs and it is the most prevalent systemic amyloidosis. Here, the authors combine biochemical and biophysical experiments to characterise the lag phase of a patient-derived truncated LC and they identify structural transitions that precede fibril formation.

    • Pamina Kazman
    • , Ramona M. Absmeier
    •  & Johannes Buchner

  • Article
    | Open Access

    Rhodobacter (Rba.) sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present the 2.9 Å cryo-EM structure of the monomeric light-harvesting-reaction center core complex from Rba. sphaeroides strain IL106, which revealed the position and conformation of PufX and the presence of an additional component protein-U, an integral membrane protein.

    • Kazutoshi Tani
    • , Kenji V. P. Nagashima
    •  & Zheng-Yu Wang-Otomo

  • 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 calcium binding protein S100B is an abundantly expressed protein in the brain and has neuro-protective functions by inhibiting Aβ aggregation and metal ion toxicity. Here, the authors combine cell biology and biochemical experiments with chemical kinetics and NMR measurements and show that S100B protein is an extracellular Tau chaperone and further characterize the interactions between S100B and Tau.

    • Guilherme G. Moreira
    • , François-Xavier Cantrelle
    •  & Cláudio M. Gomes

  • Article
    | Open Access

    The presence of the gene encoding the solute binding protein TphC has been shown to permit the uptake of terephthalate (TPA), which is the breakdown product of Polyethylene terephthalate (PET) plastic. Here the authors present a structural characterization of TphC in both open and TPA-bound closed conformations.

    • Trishnamoni Gautom
    • , Dharmendra Dheeman
    •  & Neil Dixon

  • 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

    Iron-sulfur (FeS) proteins are involved in electron transfer and CO2 fixation. Here, the authors show that FeS clusters can form spontaneously in the presence of the amino acid cysteine, in conditions similar those expected in Hadean alkaline hydrothermal vents, suggesting a plausible mechanism of their emergence at the origin of life.

    • Sean F. Jordan
    • , Ioannis Ioannou
    •  & Nick Lane

  • Article
    | Open Access

    Nuclear import receptors (NIRs) regulate self-association of RNA-binding proteins as phase modifiers, while C9orf72-derived arginine-rich polydipeptides lead to aberrant phase transitions. Here the authors show in molecular basis how arginine-rich poly-dipeptides impede the ability of NIRs, particularly Kapβ2.

    • Hitoki Nanaura
    • , Honoka Kawamukai
    •  & Eiichiro Mori

  • Article
    | Open Access

    Here, the authors use solid-state NMR and EPR measurements to characterise the ATP hydrolysis transition state of the oligomeric bacterial DnaB helicase from Helicobacter pylori, which was trapped by using aluminium fluoride as a chemical mimic. They identify protein protons that coordinate to the phosphate groups of ADP and DNA and observe that the aluminium fluoride unit is highly mobile and fast-rotating.

    • Alexander A. Malär
    • , Nino Wili
    •  & Thomas Wiegand

  • Article
    | Open Access

    The analysis of NMR spectra of complex biochemical samples with respect to individual resonances is challenging but critically important. Here, the authors present a deep learning-based method that accelerates this process also for crowded NMR data that are non-trivial to analyze, even by expert NMR spectroscopists.

    • Da-Wei Li
    • , Alexandar L. Hansen
    •  & Rafael Brüschweiler

  • Article
    | Open Access

    Aβ oligomers (AβO) are thought to represent the main toxic species in Alzheimer’s disease but very high Aβ concentrations are required to study them in vitro and it remains unknown what role these off-pathway oligomers play in vivo. Here, the authors use a dimeric variant of Aβ termed dimAβ, where two Aβ40 units are linked, which facilitates to study AβO formation kinetics and they observe that Aβ off-pathway oligomer formation is strongly accelerated at endo-lysosomal pH, while amyloid fibril formation is delayed. Furthermore, the authors demonstrate that dimAβ is a disease-relevant model construct for pathogenic AβO formation by showing that dimAβ AβOs target dendritic spines and induce AD-like somatodendritic Tau missorting.

    • Marie P. Schützmann
    • , Filip Hasecke
    •  & Wolfgang Hoyer

  • Article
    | Open Access

    The histone acetyltransferase p300 mostly localizes to active chromatin; however, some repressed genes marked with H3K27me3 are also bound by p300. Here the authors show p300 is capable of phase separation, which relies on its catalytic core, and that p300 catalytic activity is decreased in phase-separated droplets that co-localize with H3K27me3-marked chromatin.

    • Yi Zhang
    • , Kyle Brown
    •  & Tatiana G. Kutateladze

  • Article
    | Open Access

    The membrane is an integral component of the G protein-coupled receptor signaling machinery. Here authors demonstrate that lipids regulate the signaling efficacy and selectivity of the ghrelin receptor GHSR through specific interactions and bulk effects and observe PIP2 and GM3 induced shifts of the conformational equilibrium of GHSR away from its inactive state.

    • Marjorie Damian
    • , Maxime Louet
    •  & Jean-Louis Banères

  • Article
    | Open Access

    The authors generated a Synthetic Morphogenic Membrane System by encapsulating a dynamic microtubule aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. This reconstitution of artificial proto-cells reveals how non-equilibrium phenomena affect cellular information processing in morphogenesis.

    • Konstantin Gavriljuk
    • , Bruno Scocozza
    •  & Philippe I. H. Bastiaens

  • Article
    | Open Access

    Ice-nucleating proteins promote ice formation at high sub-zero temperatures, but the mechanism is still unclear. The authors investigate a model ice-nucleating protein at the air-water interface using vibrational sum frequency generation spectroscopy and simulations, revealing its reorientation at low temperatures, which increases contact with water molecules and promotes their ordering.

    • Steven J. Roeters
    • , Thaddeus W. Golbek
    •  & Tobias Weidner

  • Article
    | Open Access

    Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, which form condensates at low salt concentrations, can reenter a phase-separated regime at high salt concentrations.

    • Georg Krainer
    • , Timothy J. Welsh
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.

    • Tomoaki Kawakami
    • , Long-Jiang Yu
    •  & Zheng-Yu Wang-Otomo

  • Article
    | Open Access

    The dissociation mechanism of the heme axial ligand in heme proteins is not yet fully understood. The authors investigate the photodissociation dynamics of the bond between heme Fe and methionine S in ferrous cytochrome c using femtosecond time-resolved X-ray solution scattering and X-ray emission spectroscopy, simultaneously tracking electronic and nuclear structure changes.

    • Marco E. Reinhard
    • , Michael W. Mara
    •  & Kelly J. Gaffney

  • Article
    | Open Access

    Coiled-coil protein origami (CCPO) is a strategy for the design of polyhedral cage-shaped protein folds based on coiled-coil (CC) dimer-forming peptides. Here, the authors show that CCPO proteins fold in a multistep process governed by the spatial distance between CC modules in the primary sequence and subsequent folding intermediates, which enables the use of identical CC modules for the CCPO tetrahedron design.

    • Jana Aupič
    • , Žiga Strmšek
    •  & Roman Jerala

  • Article
    | Open Access

    Reactive oxygen species (ROS) production by reverse electron transfer (RET) through complex I is thought to cause tissue damage from heart attacks. Here, the authors combine in vivo work with biochemical and cryo-EM analyses to characterize the effects of a P25L mutation in the ND6 subunit of mitochondrial complex I. They observe that this mutation does not affect oxidative phosphorylation but renders complex I unable to generate ROS by RET: ND6-P25L mice are protected against cardiac ischaemia–reperfusion injury, thus providing evidence for the proposed role of ROS production in myocardial infarction.

    • Zhan Yin
    • , Nils Burger
    •  & Judy Hirst

  • Article
    | Open Access

    The small proton-coupled transporter EmrE confers multidrug resistance in bacteria. The structure of drug-bound EmrE in phospholipid bilayers is now determined using solid-state NMR. The structure provides detailed insights into the molecular mechanism of substrate recognition by this transporter.

    • Alexander A. Shcherbakov
    • , Grant Hisao
    •  & Mei Hong

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