Molecular conformation articles within Nature Communications

Featured

  • Article
    | Open Access

    Protein dynamics, crucial for life, are difficult and expensive to predict. This study shows that AI-based structure prediction methods can be modified for rapidly predicting the conformational landscapes of proteins, with strong correlations with experimentally-measured relative state populations.

    • Gabriel Monteiro da Silva
    • , Jennifer Y. Cui
    •  & Brenda M. Rubenstein

  • Article
    | Open Access

    In this work, the authors report a deep learning method, Deep DNAshape, to predict the influence of flanking regions on three-dimensional DNA structure and in structural readout mechanisms of protein-DNA binding.

    • Jinsen Li
    • , Tsu-Pei Chiu
    •  & Remo Rohs

  • Article
    | Open Access

    Cyclic AMP modulation of HCN channels underlies beta adrenergic stimulation of heart rate. Here, authors describe an intramolecular mechanism that controls cAMP affinity of the cyclic nucleotide binding domain of these channels.

    • Alessandro Porro
    • , Andrea Saponaro
    •  & Anna Moroni

  • Article
    | Open Access

    Bcs1, a transmembrane AAA-ATPase, facilitates the translocation of folded ISP across the inner mitochondrial membrane. This study shows that the Bcs1 ATPase cycle conformational changes are highly concerted, unlike the canonical hand-over-hand mechanism.

    • Yangang Pan
    • , Jingyu Zhan
    •  & Simon Scheuring

  • Article
    | Open Access

    CarH is a bacterial B12-binding photoreceptor involved in transcriptional regulation. Here, the authors provide insights into B12 dynamics and associated cobalt redox changes following light activation. These demonstrate the CarH response integrates light and oxygen sensing.

    • Harshwardhan Poddar
    • , Ronald Rios-Santacruz
    •  & David Leys

  • Article
    | Open Access

    Here, the authors develop a protein engineering method that enables high-resolution structural biology study of human fatty acid synthase. Using this technique, they uncover unique structural features of the enzyme and the mechanism of its inhibition by an anticancer drug Denifanstat.

    • S. M. Naimul Hasan
    • , Jennifer W. Lou
    •  & Mohammad T. Mazhab-Jafari

  • Article
    | Open Access

    Ion gradients power the neurotransmitter transport by brain glutamate transporters. Here, the authors report cryo-EM structures of the EAAT3 transporter isoform with and without the ions and the neurotransmitter, revealing the coupling mechanisms.

    • Biao Qiu
    •  & Olga Boudker

  • Article
    | Open Access

    LPL hydrolyzes triglycerides from lipoproteins. LPL can adopt many oligomeric forms. Here, the authors solve a 3.9 Å cryoEM structure of the previously uncharacterized LPL dimer. Key features include a C-terminal dimerization interface and a hydrophobic pore next to the active site.

    • Kathryn H. Gunn
    •  & Saskia B. Neher

  • Article
    | Open Access

    Combining structural, biochemical, and cellular evidence, the authors elucidate the self-recognition mechanism of a neuronal receptor sDSCAM and provide insights into the evolutionary landscape of the cell recognition molecule diversity.

    • Jie Cheng
    • , Yamei Yu
    •  & Qiang Chen

  • Article
    | Open Access

    Using a combination of MD simulations and NMR, the authors investigate how temperature affects allostery in imidazole glycerol phosphate synthase (IGPS), revealing that increase of temperature triggers local amino acid dynamics and providing insights into mechanism of allosteric regulation.

    • Federica Maschietto
    • , Uriel N. Morzan
    •  & Victor S. Batista

  • Article
    | Open Access

    It is challenging to approach protein structures in living cells. Here the authors investigate Interleukin-4 receptor alpha, which has a noncanonical amino acid incorporated at different locations, and see that evaluating click efficiency with calibrated imaging gives information on structure-related properties.

    • Frederik Steiert
    • , Peter Schultz
    •  & Thomas Weidemann

  • Article
    | Open Access

    The authors present BARASA, an approach to assign backbone triple resonance spectra of proteins that augments traditional approaches with a Bayesian statistical analysis of the observed chemical shifts. The algorithm employs a simulated annealing engine to establish a consensus set of resonance assignments and is tested against systems ranging in size to over 450 amino acids including examples of intrinsically disordered proteins.

    • Anthony C. Bishop
    • , Glorisé Torres-Montalvo
    •  & A. Joshua Wand

  • Article
    | Open Access

    In this work, the authors show that metamorphism in the post-translationally modified TDP-43 prion-like domain encodes determinants that command mechanisms with major relevance in disease and stress the relevance of post-translationally modified chains as the targets for disease intervention.

    • Jaime Carrasco
    • , Rosa Antón
    •  & Javier Oroz

  • Article
    | Open Access

    Observation of the chemical and conformational dynamics of biomolecules by diffraction methods is impeded by several physical artifacts. The authors present an extensible framework for accurate correction of such data that can keep pace with rapid developments in diffraction methods.

    • Kevin M. Dalton
    • , Jack B. Greisman
    •  & Doeke R. Hekstra

  • Article
    | Open Access

    The orientation of proteins on nanoparticle surfaces is important to the nanoparticle’s fate in vivo. Here, the authors use competitive binding between protein variants to develop a residue-based affinity scale to develop a model for the binding and orientation of proteins on gold nanoparticles

    • Joanna Xiuzhu Xu
    • , Md. Siddik Alom
    •  & Nicholas C. Fitzkee

  • 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

    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

    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

    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

    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

    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

    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

    DNA supercoiling can result in underwinding with negative supercoiling or overwinding with positive supercoiling of the DNA double helix. Here the authors reveal insights into the dynamic relationship between DNA supercoiling-induced sequence-dependent disruptions to base pairing, DNA looping, and the shape of the DNA molecule.

    • Jonathan M. Fogg
    • , Allison K. Judge
    •  & Lynn Zechiedrich

  • Article
    | Open Access

    F1Fo ATP synthase works using a rotary catalysis mechanism. Here, the authors report cryo-EM structures of Bacillus PS3 F1-ATPase encompassing the complete set of six states taken up during the catalytic cycle, including the binding- and catalytic-dwell states.

    • Meghna Sobti
    • , Hiroshi Ueno
    •  & Alastair G. Stewart

  • Article
    | Open Access

    Huntingtin exon-1 (HTTex1) consists of a N-terminal N17 domain, the disease causing polyQ domain and a C-terminal proline-rich domain (PRD). Here, the authors combine electron paramagnetic resonance (EPR), solid-state NMR with other biophysical method to characterise the structural differences of various HTTex1 fibril types with different toxicity and find that the dynamics and entanglement of the PRD domain differs among them and that the HTTex1 fibrils can be interconverted.

    • J. Mario Isas
    • , Nitin K. Pandey
    •  & Ansgar B. Siemer

  • Article
    | Open Access

    Mechanical forces acting on ligand-engaged T-cell receptors (TCRs) have previously been implicated in T-cell antigen recognition, yet their sensitivity and specificity are still poorly defined. Here, authors report a FRET-based sensor that informs directly on the magnitude and kinetics of TCR-imposed forces at the single molecule level.

    • Janett Göhring
    • , Florian Kellner
    •  & Gerhard J. Schütz

  • Article
    | Open Access

    Chromosome segregation requires the association of the kinetochore protein complex with a specialized nucleosome at the centromere. Here, the authors present cryo-EM and mutational studies that provide insights into the structure of the budding yeast centromeric nucleosome and how the centromere CBF3 protein complex guides its formation.

    • Ruifang Guan
    • , Tengfei Lian
    •  & Yawen Bai

  • Article
    | Open Access

    The conversion of auditory and vestibular stimuli into electrical signals is initiated by force transmitted to a mechanotransduction channel through the tip link. Here authors show that a single tip-link bond is more mechanically stable relative to classic cadherins, and that the double stranded tip-link connection is stabilized by single strand rebinding facilitated by strong cis-dimerization domains.

    • Eric M. Mulhall
    • , Andrew Ward
    •  & Wesley P. Wong

  • Article
    | Open Access

    p23 is a co-chaperone of Hsp90 but its mode of action is mechanistically not well understood. Here, the authors combine in vitro and yeast in vivo assays, biochemical measurements and NMR experiments to characterize p23 and identify two conserved helical elements in the intrinsically disordered C-terminal tail of p23 that together with the folded domain of p23 regulate the Hsp90 ATPase activity and affect the binding and maturation of Hsp90 clients.

    • Maximilian M. Biebl
    • , Abraham Lopez
    •  & Johannes Buchner

Browse broader subjects

Browse Molecular conformation across other nature.com journals