Solution-state NMR articles within Nature Communications

Featured

• Article
  08 May 2024 | Open Access

  Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs

  The specific recognition of a proline-rich motif in the intrinsically disordered region of SF1 by the PRPF40A tandem WW domains is modulated by an intramolecular autoinhibition, suggesting a general mechanism to enhance WW binding selectivity.

  • Santiago Martínez-Lumbreras
  • , Lena K. Träger
  •  & Michael Sattler

• Article
  07 May 2024 | Open Access

  Impact of distinct FG nucleoporin repeats on Nup98 self-association

  Here, the authors demonstrate that mutations in the FG repeats of Nup98 significantly reduce its self-association capabilities and present a cryoEM structure exhibiting higher stability per residue then previously observed, suggesting spatial variations in self-association.

  • Alain Ibáñez de Opakua
  • , Christian F. Pantoja
  •  & Markus Zweckstetter

• Article
  25 April 2024 | Open Access

  NMR characterization of RNA binding property of the DEAD-box RNA helicase DDX3X and its implications for helicase activity

  DDX3X is a member of the RNA helicase family, which remodels RNA structures. Using solution NMR, here the authors show that DDX3X preferentially binds to single-stranded RNA, which underlies its unwinding activity toward various structured RNA substrates.

  • Yuki Toyama
  •  & Ichio Shimada

• Article
  18 April 2024 | Open Access

  Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif

  Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. Here the authors obtain crystal structures and NMR data to show the recognition of diaromatic peptide motifs on a noncanonical surface of the PEX13 SH3 domain, revealing a dynamic network which modulates peroxisomal matrix import.

  • Stefan Gaussmann
  • , Rebecca Peschel
  •  & Michael Sattler

• Article
  06 April 2024 | Open Access

  Probing altered receptor specificities of antigenically drifting human H3N2 viruses by chemoenzymatic synthesis, NMR, and modeling

  Binding modes of antigenically drifted hemagglutinins of human influenza A viruses have been determined by NMR using synthetic N-glycans having ¹³C-labeled monosaccharides to pinpoint which monosaccharides of extended LacNAc chains engage with the HAs.

  • Luca Unione
  • , Augustinus N. A. Ammerlaan
  •  & Geert-Jan Boons

• Article
  20 March 2024 | Open Access

  Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE

  How do cells put electrons to rest? Using a minimal pathway to get rid of excess metabolic electrons, diverse environmentally important microbes overcome large spatial, kinetic, and thermodynamic barriers in order to survive in extreme anoxic conditions.

  • Pilar C. Portela
  • , Catharine C. Shipps
  •  & Nikhil S. Malvankar

• Article
  05 March 2024 | Open Access

  In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

  I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single stranded, cytosine-rich genomic region, but the specific contributions of several factors involved in their formation are unknown. Using in-cell NMR, the authors examined DNA i-motif formation in human cells at body temperature, suggesting i-M occur in a small portion (<1%) of genomic sites predisposed to its formation.

  • Pavlína Víšková
  • , Eva Ištvánková
  •  & Lukáš Trantírek

• Article
  02 March 2024 | Open Access

  Alternative low-populated conformations prompt phase transitions in polyalanine repeat expansions

  Here, the authors show that pathogenic mutations in the polyalanine expansions of PHOX2B promote nascent structural conformations that trigger irreversible phase transitions that arrest wild-type PHOX2B, disrupting function.

  • Rosa Antón
  • , Miguel Á. Treviño
  •  & Javier Oroz

• Article
  21 February 2024 | Open Access

  Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins

  The authors show the RNA-induced droplet formation by a component of Cajal bodies and reveal the large nanoseconds mobility of glycine residues inside droplets as a molecular factor potentially contributing to the large dynamics of Cajal bodies.

  • Giuseppe Sicoli
  • , Daniel Sieme
  •  & Nasrollah Rezaei-Ghaleh

• Article
  13 February 2024 | Open Access

  Binding kinetics drive G protein subtype selectivity at the β₁-adrenergic receptor

  The authors show G protein subtype selectivity at the β₁-adrenergic receptor is driven by the binding kinetics of ternary complex formation. Bound to G protein, the receptor adopts conformations that differ from its agonist-bound solution states.

  • Andrew J. Y. Jones
  • , Thomas H. Harman
  •  & Daniel Nietlispach

• Article
  10 February 2024 | Open Access

  Disordered regions in proteusin peptides guide post-translational modification by a flavin-dependent RiPP brominase

  Here the authors use NMR, SAXS and MD simulations to characterise the structure of proteusin peptides, which are atypically long RiPP substrates. They show a small, unstructured region in the proteusin leader is sufficient for its interaction with a halogenase that brominates the terminal tryptophan residue.

  • Nguyet A. Nguyen
  • , F. N. U. Vidya
  •  & Vinayak Agarwal

• Article
  08 February 2024 | Open Access

  The acidic intrinsically disordered region of the inflammatory mediator HMGB1 mediates fuzzy interactions with CXCL12

  Here, the authors utilise an integrative approach to characterise the fuzzy heterocomplex between CXCL12 and the fully reduced alarmin HMGB1, highlighting the importance of HMGB1’s acidic IDR to the interaction and with cell surface CXCR4.

  • Malisa Vittoria Mantonico
  • , Federica De Leo
  •  & Giovanna Musco

• Article
  20 January 2024 | Open Access

  Origin of the multi-phasic quenching dynamics in the BLUF domains across the species

  Here the authors combine 19 F NMR and femtosecond transient absorption to characterise the structural origin of the multiphasic quenching dynamics in various species of BLUF domains, highlighting the importance of the heterogeneous active-site H-bond network.

  • Yalin Zhou
  • , Siwei Tang
  •  & Dongping Zhong

• Article
  18 January 2024 | Open Access

  Molecular switching in transcription through splicing and proline-isomerization regulates stress responses in plants

  Transcription factor DREB2A interacts with Med25 to regulate stress responses. Here, the authors show that DREB2A uses splicing and proline-isomerization for this regulation and that proline cis-trans switching introduces structural frustration facilitating regulator exchange.

  • Frederik Friis Theisen
  • , Andreas Prestel
  •  & Karen Skriver

• Article
  11 January 2024 | Open Access

  Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners

  Here, the authors investigate the maturation of human respiratory Complex II, uncovering two metastable intermediates of maturation which suggest changes in intrinsic disorder ensure that the assembly steps occur in the correct sequence.

  • Pankaj Sharma
  • , Elena Maklashina
  •  & T. M. Iverson

• Article
  06 January 2024 | Open Access

  Ton motor conformational switch and peptidoglycan role in bacterial nutrient uptake

  Gram-negative bacteria rely on the Ton system for nutrient uptake. Here, authors uncover how the ExbD protein acts as a conformational switch and the function of peptidoglycan in order to energize this transport process across the outer membrane.

  • Maximilian Zinke
  • , Maylis Lejeune
  •  & Nadia Izadi-Pruneyre

• Article
  19 December 2023 | Open Access

  An RNA excited conformational state at atomic resolution

  Excited conformation state of biomolecule is transient and high-energy conformation state. Here the authors use NMR spectroscopy and computational modeling to reveal the 3D structure of HIV-1 TAR RNA excited conformational state.

  • Ainan Geng
  • , Laura Ganser
  •  & Hashim M. Al-Hashimi

• Article
  11 December 2023 | Open Access

  Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition

  The authors use an integrative structural biology approach to elucidate molecular features of the RAS Q61 family of public tumor antigens. This information can be used to develop targeted therapeutics to combat a range of cancers.

  • Andrew C. McShan
  • , David Flores-Solis
  •  & Nikolaos G. Sgourakis

• Article
  09 December 2023 | Open Access

  Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1

  GPCRs include inactive and active states. ¹⁹F-NMR and stopped-flow fluorescence kinetic assays reveal that neurotensin activates the prototypical peptide-binding GPCR, neurotensin receptor 1, through an induced-fit mechanism, where ligand binding precedes receptor conformational changes.

  • Kazem Asadollahi
  • , Sunnia Rajput
  •  & Paul R. Gooley

• Article
  29 November 2023 | Open Access

  Distinct activation mechanisms of β-arrestin-1 revealed by ¹⁹F NMR spectroscopy

  The molecular basis for the functional versatility of β-arrestins in the G-protein coupled receptor signaling pathway is not well understood. Here, the authors use¹⁹F NMR spectroscopy to show that different binding partners activate β-arrestin-1 through distinct mechanisms.

  • Ruibo Zhai
  • , Zhuoqi Wang
  •  & Yunfei Hu

• Article
  28 November 2023 | Open Access

  Unexpected dynamics in femtomolar complexes of binding proteins with peptides

  High binding affinities are usually obtained when ligands are rigidified. Here the authors present flexible peptides binding to Armadillo repeat proteins with femtomolar affinity. They demonstrate that the bound state is characterized by residual dynamics limiting entropic losses upon binding.

  • Stefano Cucuzza
  • , Malgorzata Sitnik
  •  & Oliver Zerbe

• Article
  21 November 2023 | Open Access

  Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1

  An integrated approach combing solution and solid-state NMR, molecular dynamics simulations and neutron reflectometry is applied to characterize dynamic membrane bound forms of ADP-ribosylation factor 1 (Arf1).

  • Yue Zhang
  • , Olivier Soubias
  •  & R. Andrew Byrd

• Article
  08 November 2023 | Open Access

  Mechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation

  Macrocyclic peptides were recently discovered as potent modulators of ubiquitin-mediated cellular signaling pathways. Here the authors used multidisciplinary approach to uncover how macrocyclic peptides that inhibit proteasomal degradation selectively recognize long Lys48-linked polyubiquitin chains.

  • Betsegaw Lemma
  • , Di Zhang
  •  & David Fushman

• Article
  03 November 2023 | Open Access

  DNAJB6 mutants display toxic gain of function through unregulated interaction with Hsp70 chaperones

  Here the authors characterize DNAJB6 mutants found in LGMDD1 patients. They show that these mutants retain aggregation-prevention activity, but have impaired regulation of Hsp70 binding, uncontrollably recruiting Hsp70s, depleting the chaperone levels and disrupting proteostasis.

  • Meital Abayev-Avraham
  • , Yehuda Salzberg
  •  & Rina Rosenzweig

• Article
  27 October 2023 | Open Access

  Multivalent Tau/PSD-95 interactions arrest in vitro condensates and clusters mimicking the postsynaptic density

  Cognitive impairment in Alzheimer’s disease is associated with Tau at the postsynapse. We show that multivalent Tau interactions arrest in vitro condensates and clusters mimicking the postsynaptic density that may result in synaptic dysfunction.

  • Zheng Shen
  • , Daxiao Sun
  •  & Markus Zweckstetter

• Article
  24 October 2023 | Open Access

  Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase

  In this work, the authors report a three-step charge-driven coacervation model involving dynamic complexes between a positively charged IDR of human RECQ4 and G-quadruplexes. The IDR also interacts with Replication Protein A, implying RECQ4’s regulatory role.

  • Anna C. Papageorgiou
  • , Michaela Pospisilova
  •  & Konstantinos Tripsianes

• Article
  13 October 2023 | Open Access

  Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility

  An integrated structural biology approach is utilized to elucidate the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) complexed with an internal ribosome entry site (IRES) RNA fragment from encephalomyocarditis virus (EMCV).

  • Georg Dorn
  • , Christoph Gmeiner
  •  & Frédéric H.-T. Allain

• Article
  25 September 2023 | Open Access

  Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II

  The condensation of RNA polymerase II (Pol II) into transcriptionally active clusters is critical for eukaryotic gene regulation and pre-mRNA transcription. Here the authors show that a tight network of tyrosine-proline interactions imparts temperature and concentration-dependent self-coacervation of Pol II’s C-terminal domain (CTD).

  • David Flores-Solis
  • , Irina P. Lushpinskaia
  •  & Markus Zweckstetter

• Article
  22 September 2023 | Open Access

  Acetylation discriminates disease-specific tau deposition

  The authors show that acetylation enhances the aggregation of 3R tau, while blocking the aggregation of 4R tau, providing a molecular basis for disease- and isoform-specific tau deposition.

  • Pijush Chakraborty
  • , Gwladys Rivière
  •  & Markus Zweckstetter

• Article
  07 September 2023 | Open Access

  Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy

  Here, Ye et al use high-resolution NMR in conjunction with in vitro and in vivo assays to show the catalytically important C-terminal regions of human Atg3 are conformationally dynamic and directly interact with the membrane, in collaboration with its N-terminal membrane curvature-sensitive helix.

  • Yansheng Ye
  • , Erin R. Tyndall
  •  & Fang Tian

• Article
  04 September 2023 | Open Access

  Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39

  RBM39 is an essential splicing factor for several cancer cells. Here, the authors described how RBM39 selects RNA at atomic level and autoregulates at the mRNA level by selecting the 3’-splice site of a poison exon.

  • Sébastien Campagne
  • , Daniel Jutzi
  •  & Frédéric H-T. Allain

• Article
  28 August 2023 | Open Access

  Dynamically regulated two-site interaction of viral RNA to capture host translation initiation factor

  RNA viruses use elements of their genomic RNA to commandeer the host translational machinery. Here, the authors use NMR and cryo-EM to reveal the sophisticated strategy by which a viral RNA engages host translational factors in a dynamically regulated two-site interaction.

  • Shunsuke Imai
  • , Hiroshi Suzuki
  •  & Ichio Shimada

• Article
  25 August 2023 | Open Access

  Identifying and preventing degradation in flavin mononucleotide-based redox flow batteries via NMR and EPR spectroscopy

  Aqueous organic redox-flow batteries are known to suffer capacity loss via degradation of the redox-active species. Here, the authors use in situ methods to study the electrolyte flavin mononucleotide, identifying a redox mediator mechanism that mitigates capacity loss and a route to prevent its degradation.

  • Dominic Hey
  • , Rajesh B. Jethwa
  •  & Clare P. Grey

• Article
  21 July 2023 | Open Access

  SHARPER-DOSY: Sensitivity enhanced diffusion-ordered NMR spectroscopy

  Since its discovery, the sensitivity of Nuclear Magnetic Resonance has increased steadily. Here the authors report on a liquid-state NMR methodology that increases the sensitivity of the diffusion coefficient measurements 10–100- fold, allowing to use microgram quantities of compounds, while reducing the measurement time to few minutes.

  • George Peat
  • , Patrick J. Boaler
  •  & Dušan Uhrín

• Article
  17 July 2023 | Open Access

  Molecular basis of β-lactam antibiotic resistance of ESKAPE bacterium E. faecium Penicillin Binding Protein PBP5

  Penicillin Binding Proteins (PBPs) are the main targets of β-lactam antibiotics. Here the authors use NMR spectroscopy, crystallography and microbiology to define the dynamics of E. faecium PBP5 in solution and show that increased acyl-enzyme hydrolysis correlates with increased resistance.

  • Yamanappa Hunashal
  • , Ganesan Senthil Kumar
  •  & Wolfgang Peti

• Article
  15 July 2023 | Open Access

  Structural basis for specific RNA recognition by the alternative splicing factor RBM5

  The RNA binding protein RBM5 regulates alternative splicing of genes implicated in cancer. Here the authors show structural mechanisms how multiple RNA binding domains of RBM5 cooperate to recognize specific target RNA sequences.

  • Komal Soni
  • , Pravin Kumar Ankush Jagtap
  •  & Michael Sattler

• Article
  13 July 2023 | Open Access

  Cytochrome c lysine acetylation regulates cellular respiration and cell death in ischemic skeletal muscle

  The authors report that acetylation of cytochrome c on K39 acts as a molecular switch in ischemic skeletal muscle, but not other tissues, to increase respiration and prevent apoptosis. This gives skeletal muscle robust resilience to ischemia and ischemia-reperfusion injury.

  • Paul T. Morse
  • , Gonzalo Pérez-Mejías
  •  & Maik Hüttemann

• Article
  12 July 2023 | Open Access

  AI-designed NMR spectroscopy RF pulses for fast acquisition at high and ultra-high magnetic fields

  Here, the authors utilized an evolutionary algorithm and artificial intelligence to design new basic 2D biomolecular NMR experiments to accelerate the acquisition of large biomolecular spectra. The method enables recording the spectra of poorly soluble or unstable macromolecules and analyzing the kinetics of biomolecular aggregation and oligomerization. The authors laid the foundation for accelerating multidimensional NMR experiments at high and ultra-high magnetic fields.

  • V. S. Manu
  • , Cristina Olivieri
  •  & Gianluigi Veglia

• Article
  30 June 2023 | Open Access

  Multinuclear 1D and 2D NMR with ¹⁹F-Photo-CIDNP hyperpolarization in a microfluidic chip with untuned microcoil

  The main limitations in NMR techniques are low sensitivity and the requirement for complex instrumentation. Here the authors show that a microfluidic chip with a single untuned planar spiral microcoil, combined with laser-light induced hyperpolarization, allows for multidimensional and heteronuclear Nuclear Magnetic Resonance spectroscopy on picomole quantities of material.

  • M. Victoria Gomez
  • , Sander Baas
  •  & Aldrik H. Velders

• Article
  23 June 2023 | Open Access

  Molecular mechanism of phosphopeptide neoantigen immunogenicity

  Phosphorylated peptide antigens are present on cancer cells, but their role in cancer immunity is unknown. Here, the authors describe a molecular mechanism, by which a tumor-specific phosphopeptide found in acute myeloid leukemia is recognized by the human immune T cells.

  • Yury Patskovsky
  • , Aswin Natarajan
  •  & Michelle Krogsgaard

• Article
  23 June 2023 | Open Access

  Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain variable domain protein FOR005

  Using solution-state NMR spectroscopy, the authors followed the individual steps involved in protein misfolding from the native to the amyloid fibril state for the antibody light chain (AL) amyloidosis related protein FOR005.

  • Tejaswini Pradhan
  • , Riddhiman Sarkar
  •  & Bernd Reif

• Article
  07 June 2023 | Open Access

  The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

  SARS-CoV-2 genome turnover is mediated by its N protein, but precise parameters driving the necessary RNA specificity have remained enigmatic. Here, Korn et al. reveal N’s N-terminal domain to distinguish regulatory viral RNA motifs with a preference for transiently folded elements of functional impact.

  • Sophie Marianne Korn
  • , Karthikeyan Dhamotharan
  •  & Andreas Schlundt

• Article
  07 June 2023 | Open Access

  Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314

  The authors highlight the importance of kinetics in GPCR activation. Using solution NMR, they show that the transducer βarrestin1 and the β-arrestin1biased ligand ML314 kinetically tune the conformational ensemble of the neurotensin receptor 1.

  • Fabian Bumbak
  • , James B. Bower
  •  & Joshua J. Ziarek

• Article
  05 June 2023 | Open Access

  The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase

  The function of VCP/p97 AAA-ATPase cofactor UBXD1 and its UBX domain has been elusive. Here the authors show that the extended UBXD1 UBX domain is located at the p97 pore exit where it binds ubiquitin, suggesting that UBXD1 receives unfolded substrates and hands them off for down-stream processing.

  • Mike Blueggel
  • , Alexander Kroening
  •  & Christine Beuck

• Article
  08 May 2023 | Open Access

  Inositol pyrophosphates activate the vacuolar transport chaperone complex in yeast by disrupting a homotypic SPX domain interaction

  Pipercevic et al resolve how inositol molecules activate the VTC protein complex. The VTC complex stores phosphate in yeast and is controlled by SPX domains. The inositol molecules break an interaction between SPX domains to activate the complex.

  • Joka Pipercevic
  • , Bastian Kohl
  •  & Sebastian Hiller

• Article
  20 April 2023 | Open Access

  Characterization of a fold in TANGO1 evolved from SH3 domains for the export of bulky cargos

  The authors characterized a fold in the TANGO1 protein which evolved from SH3 domains for the export of bulky cargos such as collagen. They denote this fold as MOTH (MIA, Otoraplin, TALI/TANGO1 homology) domain.

  • Oliver Arnolds
  •  & Raphael Stoll

• Article
  19 April 2023 | Open Access

  Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase

  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
  03 April 2023 | Open Access

  Unequivocal identification of two-bond heteronuclear correlations in natural products at nanomole scale by i-HMBC

  The inability to distinguish two-bond from long-range HMBC correlation has historically impeded NMR structure elucidation. Here the authors developed a practical iHMBC methodology utilizing accurate isotope shift measurement to overcome this limitation.

  • Yunyi Wang
  • , Aili Fan
  •  & Xiao Wang

• Article
  21 March 2023 | Open Access

  Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing

  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
  17 March 2023 | Open Access

  The architecture of transmembrane and cytoplasmic juxtamembrane regions of Toll-like receptors

  Toll-like receptors (TLRs) play a key role in the innate immune system. Here, Kornilov et al. resolve the 3D structures of the membrane-associated parts of four TLRs to reveal properties of the juxta-membrane domain.

  • F. D. Kornilov
  • , A. V. Shabalkina
  •  & K. S. Mineev