NMR spectroscopy articles within Nature Communications

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  • Article
    | Open Access

    Here, the authors discover that ligandability of BTB domains correlates with the presence of μs-ms time scale dynamics. This finding suggests that protein dynamics may be a broadly applicable tool in drug discovery to assess the ligandability of novel and challenging targets.

    • Vladlena Kharchenko
    • , Brian M. Linhares
    •  & Łukasz Jaremko

  • Article
    | Open Access

    Interactions between α-synuclein fibrils and lipids have been associated with the development of Parkinson’s disease. This cryo-EM study reveals structural details of these interactions and suggests a mechanism for fibril-induced lipid extraction.

    • Benedikt Frieg
    • , Leif Antonschmidt
    •  & Gunnar F. Schröder

  • Article
    | Open Access

    In this work the authors report the structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The study provides insights into the dynamic changes under which the neck linker goes upon binding to ADP.

    • Chunting Zhang
    • , Changmiao Guo
    •  & Tatyana Polenova

  • Article
    | Open Access

    In this manuscript the authors report accurate multi-state protein structures of the PDZ domain using biological NMR. By looking into protein structural states, the authors report an allosteric pathway at atomic resolution that validates previously reported low resolution findings and uncovered a structural hallmark of the allosteric ligand binding to the PDZ domain.

    • Dzmitry Ashkinadze
    • , Harindranath Kadavath
    •  & Roland Riek

  • Article
    | Open Access

    The analysis of protein NMR spectra is time-consuming and can occupy a human expert for weeks or months. The researchers in this work present a deep learning-based method that delivers signal positions, chemical shift assignments, and structures of proteins within hours after completion of the NMR measurements.

    • Piotr Klukowski
    • , Roland Riek
    •  & Peter Güntert

  • Article
    | Open Access

    Phosphorylation at multiple sites is a major regulatory mechanism in cellular signalling. Here, the authors show that multisite phosphorylation of the c-JUN transcription factor by the JNK kinase exhibits intrinsic kinetics that allow a precise and timed regulation of the transcriptional output.

    • Christopher A. Waudby
    • , Saul Alvarez-Teijeiro
    •  & Anastasia Mylona

  • Article
    | Open Access

    The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. Herein, the authors report the NMR solution structures of a bulge-containing KRAS-G4 that bound to two small molecules. The study provides molecular details of ligand interactions with KRAS-G4 and contributes insight into the design of specific KRAS-G4-interactive drugs.

    • Kai-Bo Wang
    • , Yushuang Liu
    •  & Ling-Yi Kong

  • Article
    | Open Access

    The authors report an unusual mode of AU-rich RNA recognition by the RNA recognition motifs of DND1, a protein essential for germline development, in a 27.5 kDa NMR structure and provide additional insight on DND1 function from cell-based experiments.

    • Malgorzata M. Duszczyk
    • , Harry Wischnewski
    •  & Frédéric H.-T. Allain

  • Article
    | Open Access

    Influenza A virus (IAV) nonstructural protein 1 (NS1) is a multifunctional virulence factor that interacts with several host factors such as phosphatidylinositol-3-kinase (PI3K). NS1 binds specifically to the p85β regulatory subunit of PI3K and subsequently activates PI3K signaling. Here, Kim et al. show that functionally near-neutral, strain-specific NS1 mutations lead to variations in binding kinetics to p85β exhibit long-range epistatic interactions. Applying NMR they provide evidence that the structural dynamics of the NS1 hydrophobic core have evolved over time and contributed to epistasis.

    • Iktae Kim
    • , Alyssa Dubrow
    •  & Jae-Hyun Cho

  • Article
    | Open Access

    Quantum sensors based on NV centers in diamond find applications in high spatial resolution NMR spectroscopy, but their operation is typically limited to low fields. Sahin et al. demonstrate a high-field sensor based on nuclear spins in diamond, where NV centers play a supporting role in optical initialization.

    • Ozgur Sahin
    • , Erica de Leon Sanchez
    •  & Ashok Ajoy

  • Article
    | Open Access

    Ubiquitin is not only a posttranslational modifier but itself is subject to modifications, such as acetylation. Characterization of distinct acetylated ubiquitin variants reveals that each acetylation site has a particular impact on ubiquitin structure and its protein-protein interaction properties.

    • Simon Maria Kienle
    • , Tobias Schneider
    •  & Martin Scheffner

  • Article
    | Open Access

    Understanding how small molecules bind to pathological aggregates is of importance for therapeutic and diagnostic development in diseases such as Parkinson’s Disease. Here, the authors reveal a binding site of anle138b to lipid-induced α-synuclein fibrils.

    • Leif Antonschmidt
    • , Dirk Matthes
    •  & Loren B. Andreas

  • Article
    | Open Access

    Unwanted RNA transcripts are targeted for degradation by nuclear complexes such as MTREC/PAXT. Here, the authors structurally and functionally characterized three interfaces of the scaffold protein Red1, providing mechanistic insights into conserved features of MTREC/PAXT architecture.

    • Anne-Emmanuelle Foucher
    • , Leila Touat-Todeschini
    •  & Jan Kadlec

  • 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

    Entomopathogenic bacteria used for pest control secrete potent Tc toxins. Here, the authors combine biochemistry, solution and solid-state NMR spectroscopy and cryo-EM to show in atomic detail how the toxin disrupts the host cell cytoskeleton and kills the target cell.

    • Alexander Belyy
    • , Florian Lindemann
    •  & Stefan Raunser

  • Article
    | Open Access

    The authors provide a litmus test for the recognition mechanism of transiently binding proteins based on nuclear magnetic resonance and find a conformational selection binding mechanism through concentration-dependent kinetics of ubiquitin and SH3.

    • Kalyan S. Chakrabarti
    • , Simon Olsson
    •  & Christian Griesinger

  • Article
    | Open Access

    Alzheimer’s disease is characterized by the accumulation of aggregated tau protein. Here the authors find that Hsp chaperones, which normally protect cell homeostasis, can assemble with co-chaperones in a “multichaperone machinery” to target tau aggregation.

    • Antonia Moll
    • , Lisa Marie Ramirez
    •  & Markus Zweckstetter

  • Article
    | Open Access

    Molecules offer enormous capacity for information storage. Here, the authors show that information can be encoded into molecules with sequences of paramagnetic lanthanide ions, and decoded using nuclear magnetic resonance spectroscopy.

    • Jan Kretschmer
    • , Tomáš David
    •  & Miloslav Polasek

  • Article
    | Open Access

    Here the authors report that the Taf2 and Taf14 subunits of the yeast TFIID complex interact and mediate binding to chromatin. Binding of Taf2 to Taf14 promotes a conformational rearrangement in Taf14, resulting in a release of the linker region for the engagement with the nucleosome and their association with DNA is essential for transcriptional regulation.

    • Brianna J. Klein
    • , Jordan T. Feigerle
    •  & Tatiana G. Kutateladze

  • 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

    How ATP-independent chaperones release their clients without energy input remains enigmatic. Here the authors discover that chaperone Spy uses its long, disordered N terminus to facilitate client release through competitive, dynamic intramolecular interactions with Spy’s client binding surface.

    • Wei He
    • , Xinming Li
    •  & Shu Quan

  • Article
    | Open Access

    The authors report here that talin and kindlin, the two key integrin binders and activators, are bridged by paxillin to induce microclustering of integrins to potently bind to multivalent extracellular ligand and trigger rapid cell attachment.

    • Fan Lu
    • , Liang Zhu
    •  & Jun Qin

  • Article
    | Open Access

    Despite their relevance as regulators of actin severing and filament disassembly, few structural insights into the mechanism of cofilin-isoform-specific severing activity are reported. Here, the authors provide structural insights towards actin severing activity by human cofilin-2 obtained by MAS NMR and all-atom MD simulations. The results reveal an isoform-specific binding mode unique to CFL2 that may be related to its potent severing properties in-vivo.

    • Jodi Kraus
    • , Ryan W. Russell
    •  & Tatyana Polenova

  • 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

    RNA molecules exhibit conformational fluctuations between ground states and excited states. Here the authors designed and verified small hairpin RNAs with predefined secondary structure reshufflings. In light of Van’t Hoff analysis and accelerated molecular dynamics simulation, a mechanism of multistep sequential transition has been revealed.

    • Ge Han
    •  & Yi Xue

  • Article
    | Open Access

    The permeability barrier of nuclear pores is formed by disordered and yet self-interacting FG repeat domains, whose sequence heterogeneity is a challenge for mechanistic insights. Here the authors overcome this challenge and characterize the protein’s dynamics by applying NMR techniques to an FG phase system that has been simplified to its essentials.

    • Eszter E. Najbauer
    • , Sheung Chun Ng
    •  & Loren B. Andreas

  • Article
    | Open Access

    Phosphate involvement in calcium carbonate biominerals raises questions on biomineralisation pathways. Here, the authors explore the presence of phosphate in the growing shell of the European abalone and suggest a shared mixed mineral ancestral precursor with final crystal phase being selected by mineral-associated proteins.

    • Widad Ajili
    • , Camila B. Tovani
    •  & Nadine Nassif

  • Article
    | Open Access

    Nuclear magnetic resonance imaging at the atomic scale has been limited to detection and localisation of single nuclear spins. Here, the authors extend imaging to large nuclear spin clusters in 3D by combining weak quantum measurements, phase encoding and simulated annealing.

    • K. S. Cujia
    • , K. Herb
    •  & C. L. Degen

  • Article
    | Open Access

    Many bacteria can take up exogenous DNA, in a process that often requires surface appendages composed of thousands of protein subunits called pilins. Here, Braus et al. show that a minor pilin binds directly to DNA and is important for DNA uptake in the pathogen Legionella pneumophila.

    • Sebastian A. G. Braus
    • , Francesca L. Short
    •  & Manuela K. Hospenthal

  • Article
    | Open Access

    G-wire structures have potential applications in bio-nanotechnology, however, this is limited by a lack of understanding about the assembly process and structures formed. Here, the authors use nuclear magnetic resonance and molecular dynamic simulations to understand the guiding principles of G-wire assembly.

    • Daša Pavc
    • , Nerea Sebastian
    •  & Primož Šket

  • Article
    | Open Access

    Time-resolved NMR spectra provide unique structural and dynamical information, but their measurement in systems undergoing chemical reactions is challenging. Here the authors, combining single-scan spectroscopic imaging, rapid mixing and continuous flow techniques, obtain chemically resolved snapshots of a reacting system throughout the reaction coordinate.

    • Michael J. Jaroszewicz
    • , Mengxiao Liu
    •  & Lucio Frydman

  • Article
    | Open Access

    The intracellular domain (ICD) of Cys-loop receptors mediates many of their functions, but no complete structure of a Cys-loop receptor ICD is available to date. Here, the authors combine NMR and ESR spectroscopy to determine the full-length ICD structures of the human α7 nicotinic acetylcholine receptor (α7nAChR).

    • Vasyl Bondarenko
    • , Marta M. Wells
    •  & Pei Tang

  • Article
    | Open Access

    The cell wall of the bacterial pathogen Group A Streptococcus is decorated with a polysaccharide termed GAC, which is a target for vaccine development. Here, Rush et al. characterize the linkage between GAC and peptidoglycan, and identify a protein that deacetylates the linkage and thus protects the pathogen against host cationic antimicrobial proteins.

    • Jeffrey S. Rush
    • , Prakash Parajuli
    •  & Natalia Korotkova

  • Article
    | Open Access

    The plant biomass is a composite formed by a variety of polysaccharides and an aromatic polymer named lignin. Here, the authors use solid-state NMR spectroscopy to unveil the carbohydrate-aromatic interface that leads to the variable architecture of lignocellulose biomaterials.

    • Alex Kirui
    • , Wancheng Zhao
    •  & Tuo Wang

  • Article
    | Open Access

    TCPTP is a non-receptor type protein tyrosine phosphatase involved in various signalling pathways. Here, the authors provide structural insights into TCPTP activation, showing that TCPTP is inhibited by its C-terminal tail, which can be displaced by the cytosolic tail of integrin-α1, leading to activation.

    • Jai Prakash Singh
    • , Yang Li
    •  & Tzu-Ching Meng

  • Article
    | Open Access

    The authors present a strategy to construct dynamic biomolecular landscapes. Here, they derive a quantitative description of the distribution timescales and amplitudes of reorientational motion of POPC membranes from the combination of NMR relaxation data and frame analysis of MD simulations.

    • Albert A. Smith
    • , Alexander Vogel
    •  & Daniel Huster

  • Article
    | Open Access

    Rpn13 is a substrate receptor of the 26S proteasome and an anti-cancer drug target. Here, the authors identify and characterize XL5, a lead compound that binds to the N-terminal Pru domain of human Rpn13 (hRpn13), solve the NMR structure of XL5-ligated hRpn13 Pru and develop XL5-PROTACs that preferentially target an identified hRpn13 Pru fragment present in multiple myeloma cells.

    • Xiuxiu Lu
    • , Venkata R. Sabbasani
    •  & Kylie J. Walters

  • Article
    | Open Access

    β-arrestins commonly bind to two distinct elements in GPCRs: the phosphorylated carboxyl terminal tail (C tail) and the cytoplasmic face of the transmembrane region (TM core). Here, the authors use methyl-TROSY NMR measurements to characterise the interactions between β-arrestin 1 (βarr1) and a GPCR and observe that C tail-mediated interaction with a GPCR alone induces the partial activation of βarr1, whereas the TM core- and C tail-mediated interactions together stabilize the activated conformation of βarr1.

    • Yutaro Shiraishi
    • , Yutaka Kofuku
    •  & Ichio Shimada

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