NMR spectroscopy

  • Article
    | Open Access

    Studying the unfolding of membrane proteins in a native-like lipid environment is challenging. Here the authors describe a method combining hydrogen-deuterium exchange and solid-state NMR measurements that allows the characterization of unfolding events in lipid-embedded membrane proteins and use the photoreceptor Anabaena Sensory Rhodopsin as a test case.

    • Peng Xiao
    • , David Bolton
    •  & Vladimir Ladizhansky
  • Article
    | Open Access

    Autophagy mediated by the conjugation pathway for ubiquitin-like proteins plays a key role in controlling homeostasis in eukaryotic cells. Here the authors provide a molecular basis for allosteric activation of the E2 ligase Atg3, uncovering the mechanism underlying Atg8 lipidation and a novel mechanism regulating E1-E2-E3-mediated ubiquitin-like protein conjugation.

    • Yumei Zheng
    • , Yu Qiu
    •  & Brenda A. Schulman
  • Article
    | Open Access

    Hsp chaperones stabilize the inactive conformation of androgen receptor (AR) and are released upon hormone-induced AR activation. Here, the authors locate the Hsp binding region on AR, and show that Hsp70 reduces AR aggregation and promotes AR degradation in cellular and mouse models of a neuromuscular disorder.

    • Bahareh Eftekharzadeh
    • , Varuna C. Banduseela
    •  & Xavier Salvatella
  • Article
    | Open Access

    Electron diffraction can be used to determine nanocrystal structures, but is unsuitable for locating hydrogen atoms. Here the authors combine electron diffraction, solid-state NMR and first-principles calculations to resolve the crystal structures and hydrogen-bonding networks of L-histidine and cimetidine form B.

    • Candelaria Guzmán-Afonso
    • , You-lee Hong
    •  & Yusuke Nishiyama
  • Article
    | Open Access

    Transfer RNA (tRNA) is regulated by RNA modifications. Here the authors employ time-resolved NMR to monitor modifications of yeast tRNAPhe in cellular extracts, revealing a sequential order and cross-talk between modifications.

    • Pierre Barraud
    • , Alexandre Gato
    •  & Carine Tisné
  • Article
    | Open Access

    CARD9 and CARD11 propagate signaling by nucleating Bcl10 polymerization in immune cells and are both held in an autoinhibited state prior to activation. Here, the authors combine structural, biochemical, and cell-based approaches to reveal the structural basis for CARD9/11 autoinhibition and show that the two proteins are activated through similar but distinct mechanisms.

    • Michael J. Holliday
    • , Axel Witt
    •  & Wayne J. Fairbrother
  • Perspective
    | Open Access

    Lack of best practice guidelines currently limits the application of metabolomics in the regulatory sciences. Here, the MEtabolomics standaRds Initiative in Toxicology (MERIT) proposes methods and reporting standards for several important applications of metabolomics in regulatory toxicology.

    • Mark R. Viant
    • , Timothy M. D. Ebbels
    •  & Ralf J. M. Weber
  • Article
    | Open Access

    Zero-field nuclear magnetic resonance can identify species and collective behaviors in mixtures without applied magnetic fields. Here the authors demonstrate its use for resolving proton exchange in ammonium and for the detection of hyperpolarized pyruvic acid, an important imaging biomarker.

    • Danila A. Barskiy
    • , Michael C. D. Tayler
    •  & Alexander Pines
  • Article
    | Open Access

    Processing bodies (P-bodies) are non-membrane-bound protein/RNA granules in the cytosol. Here the authors combine bioinformatics, NMR and cell based assays and find that lysine is enriched in the disordered regions of P-body-associated proteins and show that lysine-rich polypeptides form highly dynamic lysine/RNA-coacervates and lysine acetylation reverses liquid-liquid phase separation.

    • Tina Ukmar-Godec
    • , Saskia Hutten
    •  & Markus Zweckstetter
  • Article
    | Open Access

    The ligand-activated transcription factor farnesoid X receptor (FXR) acts as a cellular sensor for bile acids and is of interest as a drug target. Here the authors employ X-ray crystallography and NMR to characterize the molecular determinants of FXR agonists, antagonists and a partial agonist that drive FXR activation and antagonism.

    • Daniel Merk
    • , Sridhar Sreeramulu
    •  & Harald Schwalbe
  • Article
    | Open Access

    NMR structure determination is challenging for proteins with a molecular weight above 30 kDa and atomic-resolution structure determination from cryo-EM data is currently not the rule. Here the authors describe an integrated structure determination approach that simultaneously uses NMR and EM data and allows them to determine the structure of the 468 kDa dodecameric aminopeptidase TET2 complex.

    • Diego F. Gauto
    • , Leandro F. Estrozi
    •  & Jerome Boisbouvier
  • Article
    | Open Access

    Entropic ligands can dramatically improve the solubility of nanocrystals, but it is not known how these mixed ligand systems actually arrange and interact on a particle surface. Here, the authors use advanced solid-state NMR techniques to understand the partitioning and dynamics of entropic mixed ligand shells on CdSe nanocrystals, and relate this molecular picture to the particles’ macroscopic solubility behavior.

    • Zhenfeng Pang
    • , Jun Zhang
    •  & Xiaogang Peng
  • Article
    | Open Access

    Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.

    • Victor A. Streltsov
    • , Sukanya Luang
    •  & Maria Hrmova
  • Article
    | Open Access

    Polyglutamine (polyQ) tracts are low-complexity regions and their expansion is linked to certain neurodegenerative diseases. Here the authors combine experimental and computational approaches to find that the length of the androgen receptor polyQ tract correlates with its helicity and show that the polyQ helical structure is stabilized by hydrogen bonds between the Gln side chains and main chain carbonyl groups.

    • Albert Escobedo
    • , Busra Topal
    •  & Xavier Salvatella
  • Article
    | Open Access

    Opening of G protein-gated inwardly rectifying potassium channels (GIRK) is coupled to the activation of a GPCR. Here the authors use NMR and cell-based BRET assays to gain insights into the mechanisms underlying family-specific activation and find that pre-formation of the Gαi/oβγ-GIRK complex in the inactive state is responsible for specific GIRK activation and present a structural model for the Gαi/oβγ-GIRK complex.

    • Hanaho Kano
    • , Yuki Toyama
    •  & Ichio Shimada
  • Article
    | Open Access

    Dissolution-dynamic nuclear polarization is able to enhance nuclear magnetic resonance signals, but requires complex procedures to generate hyperpolarized nuclear spins. Here the authors establish a fast and facile method to transfer hyperpolarized samples into the liquid solution where the measurement is performed.

    • Karel Kouřil
    • , Hana Kouřilová
    •  & Benno Meier
  • Article
    | Open Access

    Analysis of side-chain motions by NMR has so far been restricted to small proteins and methyl-bearing side chains. Here, the authors present NMR methods based on 13C direct detection of highly deuterated protein samples that yield sharp and well-resolved signals and allow the characterisation of side-chain conformational dynamics of six different amino acid types in medium-to-large proteins.

    • Ruth B. Pritchard
    •  & D. Flemming Hansen
  • Article
    | Open Access

    Ubiquitination of histone H2A can occur on distinct lysine residues, but how each site is recognised by the specific E3 ligase remains poorly understood. Here the authors demonstrate that the E3 ligase RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine K13/K15.

    • Velten Horn
    • , Michael Uckelmann
    •  & Hugo van Ingen
  • Article
    | Open Access

    The cyclin-dependent kinase (Cdk) inhibitor p27Kip1 (p27) folds upon binding to Cdk/cyclin complexes and during cell cycle progression p27 becomes phosphorylated, which triggers its ubiquitination and degradation. Here the authors use an integrated approach and show that Cdk2/cyclin A-bound p27 samples lowly-populated conformations that dynamically anticipate the sequential steps of the signaling cascade.

    • Maksym Tsytlonok
    • , Hugo Sanabria
    •  & Richard Kriwacki
  • Article
    | Open Access

    Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection. Here the authors report that an asparagine residue located near the HBGA-attachment site can convert into an iso-aspartate residue through spontaneous deamidation and influence HBGA recognition.

    • Alvaro Mallagaray
    • , Robert Creutznacher
    •  & Thomas Peters
  • Article
    | Open Access

    The cellular functions of arrestins are determined in part by the pattern of phosphorylation on the G protein-coupled receptors (GPCRs) to which arrestins bind. Here, authors use a library of synthetic phosphopeptide analogues of the GPCR rhodopsin C-terminus and determine the ability of these peptides to bind and activate arrestins using a variety of biochemical and biophysical methods.

    • Daniel Mayer
    • , Fred F. Damberger
    •  & Dmitry B. Veprintsev
  • Article
    | Open Access

    The small heat-shock protein HSP27 occurs predominantly in oligomeric forms, which makes its structural characterisation challenging. Here the authors employ CPMG and high-pressure NMR with native mass spectrometry and biophysical assays to show that the active monomeric form of HSP27 is substantially disordered and highly chaperone-active.

    • T. Reid Alderson
    • , Julien Roche
    •  & Andrew J. Baldwin
  • Article
    | Open Access

    The halogen bond is well known for its ability to assemble supramolecules. Here, using NMR experiments, the authors reveal the role of these bonds in dynamic processes, finding that the halogen bond directly catalyzes dynamical rotation in solid cocrystals by reducing the associated energy barrier.

    • Patrick M. J. Szell
    • , Scott Zablotny
    •  & David L. Bryce
  • Article
    | Open Access

    Allosteric interactions are an important contributor to the catalytic properties of enzyme. Here the authors demonstrate—using the prototypical protein kinase PKA—that the allosteric cooperativity underscoring substrate recognition and product release are directly linked to changes in conformational entropy.

    • Yingjie Wang
    • , Manu V.S.
    •  & Gianluigi Veglia
  • Article
    | Open Access

    Serine/threonine phosphatases such as PP1 associate with a large array of subunit proteins, such as ASPP (apoptosis-stimulating protein of p53) to achieve selective targeting. Here authors solved the crystal structure of the human ASPP2/PP1 complex and explain how ASPP2 can distinguish between PP1 isoforms.

    • M. Teresa Bertran
    • , Stéphane Mouilleron
    •  & Nicolas Tapon
  • Article
    | Open Access

    The antitermination factor RfaH adopts two functional states where its C-terminal domain is folded either as an α-helical hairpin or β-barrel. Here the authors employ solution state NMR measurements to show that the C-terminal domain transforms into the β-barrel only upon binding to the elongation complex and refolds back after dissociation.

    • Philipp Konrad Zuber
    • , Kristian Schweimer
    •  & Stefan H. Knauer
  • Article
    | Open Access

    Designing interfaces that can induce protein-protein interactions is a challenging problem. Here the authors show that a five amino acid sequence known to mediate domain swapping in cystatins can drive oligomerization when grafted onto functionally and structurally unrelated host proteins, providing a simple approach to the design of protein assemblies.

    • Neha Nandwani
    • , Parag Surana
    •  & Shachi Gosavi
  • Article
    | Open Access

    The interactions of lignin with polysaccharides in plant secondary cell walls are not well understood. Here the authors employ solid-state NMR measurements to analyse intact stems of maize, Arabidopsis, switchgrass and rice and observe that lignin self-aggregates and forms highly hydrophobic microdomains that make extensive surface contacts to xylan.

    • Xue Kang
    • , Alex Kirui
    •  & Tuo Wang
  • Article
    | Open Access

    Transient oligomeric species of the amyloid-β peptide (Aβ42) have been identified as key pathogenic agents in Alzheimer’s disease. Here the authors find that the aminosterol trodusquemine enhances Aβ42 aggregation and suppresses Aβ42-induced toxicity by displacing oligomers from cell membranes.

    • Ryan Limbocker
    • , Sean Chia
    •  & Christopher M. Dobson
  • Article
    | Open Access

    Spontaneous activity shifts at constant experimental conditions are widespread among ion channels but the molecular origins are poorly understood. Here, using solid-state NMR and MD simulations, the authors reveal that modal gating shifts in K + channels are caused by large shifts in the channel dynamics which perturb the selectivity filter.

    • Shehrazade Jekhmane
    • , João Medeiros-Silva
    •  & Markus Weingarth
  • Article
    | Open Access

    DnaB helicases are motor proteins that couple ATP-hydrolysis to the movement of the protein along single-stranded DNA leading to a separation of double-stranded DNA at the replication fork. Here authors use solid-state NMR spectroscopy and reveal DnaB’s conformational responses to ATP hydrolysis and the resulting DNA loading and translocation.

    • Thomas Wiegand
    • , Riccardo Cadalbert
    •  & Beat H. Meier
  • Article
    | Open Access

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a target for insulin sensitizing drugs. Here the authors combine NMR, X-ray crystallography and MD simulations and report a structural mechanism for eliciting PPARγ inverse agonism, where coactivator binding is inhibited and corepressor binding promoted, which causes PPARγ repression.

    • Richard Brust
    • , Jinsai Shang
    •  & Douglas J. Kojetin
  • Article
    | Open Access

    The chaperone Hsp90 plays a key role in maintaining cellular homeostasis. Here the authors provide structural insights into substrate recognition and the pro-folding mechanism of Hsp90/co-chaperone complexes by studying the complex of Hsp90 with its co-chaperone FKBP51 and the substrate Tau bound Hsp90/FKBP51 ternary complex using a NMR based integrative approach.

    • Javier Oroz
    • , Bliss J. Chang
    •  & Markus Zweckstetter
  • Article
    | Open Access

    The protein tyrosine phosphatase SHP2 is a key regulator of cell cycle control. Here the authors combine NMR measurements and X-ray crystallography and show that wild-type SHP2 dynamically exchanges between a closed inactive conformation and an open activated form and that the oncogenic E76K mutation shifts the equilibrium to the open state, which is reversed by binding of the allosteric inhibitor SHP099.

    • Ricardo A. P. Pádua
    • , Yizhi Sun
    •  & Dorothee Kern
  • Article
    | Open Access

    Impaired kidney function can lead to an increase of β2-microglobulin (β2m) serum levels, which can cause β2m aggregation and amyloid fibril formation. Here the authors combine cryo-EM and magic angle spinning NMR measurements to determine the structure of a β2m fibril and they also present the low resolution model of a β2m fibril with a different morphology.

    • Matthew G. Iadanza
    • , Robert Silvers
    •  & Sheena E. Radford