Molecular conformation articles within Nature Communications

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  • Article
    | Open Access

    Our understanding of the molecular mechanisms underlying pathological protein aggregation remains incomplete. Here, single molecule infrared nanospectroscopy (AFM-IR) offers insight into the structure of Aβ42 oligomeric and fibrillar species and their interaction with an aggregation inhibitor, paving the way for single molecule drug discovery studies.

    • Francesco Simone Ruggeri
    • , Johnny Habchi
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    β-phosphoglucomutase (βPGM) from Lactococcus lactis is a phosphoryl transfer enzyme required for catabolism of trehalose and maltose. Coupled analyses of multiple βPGM structures and enzymatic activity lead to the proposal of allomorphy — a post-translational mechanism controlling enzyme activity.

    • Henry P. Wood
    • , F. Aaron Cruz-Navarrete
    •  & Jonathan P. Waltho

  • Article
    | Open Access

    Protein structural dynamics can be studied by time-resolved crystallography (TRC) and ultrafast transient spectroscopic methods. Here, the authors perform electronic and vibrational transient absorption measurements to characterise the full photocycle of Photoactive Yellow Protein (PYP) both in the crystalline and solution state and find that the photocycle kinetics and structural intermediates of PYP deviate in the crystalline state, which must be taken into consideration when planning TRC experiments.

    • Patrick E. Konold
    • , Enis Arik
    •  & Marie Louise Groot

  • Article
    | Open Access

    Human Histone Deacetylases (HDACs) regulate gene expression and are important drug targets. Here, the authors combine NMR measurements, enzymatic assays and molecular dynamics simulations and show that HDAC8 samples a catalytically active and an inactive state and further demonstrate that mutations and ligand binding alter the populations of the two states, which is of interest for inhibitor design.

    • Nicolas D. Werbeck
    • , Vaibhav Kumar Shukla
    •  & D. Flemming Hansen

  • Article
    | Open Access

    Menthol in mints elicits a coolness sensation by selective activation of TRPM8 ion channel. Here authors dock menthol to TRPM8 and systematically validate their menthol binding models with thermodynamic mutant cycle analysis in functional tests, and shed light on TRPM8 activation by menthol at the atomic level.

    • Lizhen Xu
    • , Yalan Han
    •  & Fan Yang

  • Article
    | Open Access

    Microtubules are dynamic tubulin polymers which elongate by addition of bent guanosine triphosphate tubulin to the tips of curving protofilaments. Here authors use Brownian dynamics modeling and electron cryotomography to show that the lateral activation energy barrier in tubulin-tubulin interactions is a key parameter for this process, controlling the development of high pulling forces.

    • Nikita B. Gudimchuk
    • , Evgeni V. Ulyanov
    •  & J. Richard McIntosh

  • Article
    | Open Access

    While infrared nanospectroscopy methods based on thermomechanical detection (AFM-IR) enables the acquisition of absorption spectra at the nanoscale, single molecule detection has not been possible so far. Here, the authors present off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR), which allows measuring infrared absorption spectra at the single molecule level in a time scale of seconds with high throughput and demonstrate that the secondary structure of single protein molecules can be determined with this method.

    • Francesco Simone Ruggeri
    • , Benedetta Mannini
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    The movement of cytoplasmic dynein on microtubule tracks is coordinated by the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk. Here authors use NMR and cryo-EM and suggest that the communication between the ATPase-domain and MTBD is achieved by sliding of the stalk α-helix by a half-turn or one-turn.

    • Noritaka Nishida
    • , Yuta Komori
    •  & Masahide Kikkawa

  • Article
    | Open Access

    To carry out their function, transcription factors must efficiently recognize specific DNA sequence targets, a complex problem in the context of eukaryotic chromatin. Here the authors use single-molecule biophysical experiments, statistical mechanical theory and bioinformatics analyses to conclude that interactions with non-target sequences near promoters serve to increase overall affinity and targeting efficiency.

    • Milagros Castellanos
    • , Nivin Mothi
    •  & Victor Muñoz

  • Article
    | Open Access

    Riboswitches bind intracellular metabolites and control bacterial gene expression. Here, by using X-ray crystallography, molecular dynamics simulations, and single-molecule fluorescence resonance energy transfer, the authors show how a local Mn2+ ion-binding signal is transduced across the yybP-ykoY riboswitch from Xanthomonas oryzae.

    • Krishna C. Suddala
    • , Ian R. Price
    •  & Nils G. Walter

  • Article
    | Open Access

    Microtubules (MTs) are well-studied cytoskeleton components, but have primarily been investigated using fixation or invasive techniques. Here, the authors use label-free second harmonic (SH) fluorescence and correlative light electron microscopy to pinpoint determinants required for SH from MTs.

    • V. Van Steenbergen
    • , W. Boesmans
    •  & P. Vanden Berghe

  • 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 biological functions of lipids critically depend on their highly diverse molecular structures. Here, the authors determine the mass-resolved collision cross sections of 456 sphingolipid and glycerophospholipid species, providing a reference for future structural lipidomics studies.

    • Katrina L. Leaptrot
    • , Jody C. May
    •  & John A. McLean

  • Article
    | Open Access

    Somatic mutations within antibody framework regions (FWR) can alter structural flexibility, but their role in maturation of broadly neutralizing antibodies (bnAbs) is unclear. Here the authors show how FWR mutations impact interdomain conformational flexibility and paratope plasticity during bnAb development.

    • Rory Henderson
    • , Brian E. Watts
    •  & S. Munir Alam

  • Article
    | Open Access

    IRSp53 is a key regulator of filopodia formation and cell migration. Here, the authors elucidate a mechanism of phosphorylation-dependent inhibition of IRSp53 by 14-3-3, which impedes the interactions of IRSp53 with membranes and downstream cytoskeletal effectors.

    • David J. Kast
    •  & Roberto Dominguez

  • Article
    | Open Access

    Allostery is a fundamental principle of protein regulation that remains challenging to engineer. Here authors screen human Inward Rectifier K + Channel Kir2.1 for permissibility to domain insertions and propose that differential permissibility is a metric of latent allosteric capacity in Kir2.1.

    • Willow Coyote-Maestas
    • , Yungui He
    •  & Daniel Schmidt

  • Article
    | Open Access

    Phytochromes are photoreceptors that are present in plants, bacteria and fungi. Here the authors present crystal structures of the phytochrome Agp2 from Agrobacterium fabrum in the parent Pfr state as well as a functional Meta-F intermediate and discuss mechanistic implications for photoconversion.

    • Andrea Schmidt
    • , Luisa Sauthof
    •  & Patrick Scheerer

  • Article
    | Open Access

    How interactions between binding partners form or break is hidden in the transition paths from the encounter to the formation of a stable complex. Here authors use single‐molecule spectroscopy to measure the transition path times for the association of two intrinsically disordered proteins that form a folded dimer upon binding and identify a metastable encounter complex.

    • Flurin Sturzenegger
    • , Franziska Zosel
    •  & Benjamin Schuler

  • Article
    | Open Access

    Generation and iterative optimization of designed enzymes can provide valuable insights for a more efficient catalysis. Here the authors have followed the iterative improvement of a designed Kemp eliminase and show that remote point mutations could remodel the designed active site via substantial conformational reorganization.

    • Nan-Sook Hong
    • , Dušan Petrović
    •  & Colin J. Jackson

  • Article
    | Open Access

    The SNARE complex enables the fusion of synaptic vesicles with presynaptic membrane via a zippering process that is modulated by the protein complexin, though the precise mechanism remains unclear. Here, the authors used magnetic tweezers to show how complexin prepares a SNARE complex for fusion under mechanical tension.

    • Min Ju Shon
    • , Haesoo Kim
    •  & Tae-Young Yoon

  • Article
    | Open Access

    Mutations in the cation channel PKD2 cause human autosomal dominant polycystic kidney disease but its channel function and gating mechanism are poorly understood. Here authors study PKD2 using electrophysiology and cryo-EM, which identifies hydrophobic gates and proposes a gating mechanism for PKD2.

    • Wang Zheng
    • , Xiaoyong Yang
    •  & Xing-Zhen Chen

  • Article
    | Open Access

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor. Here the authors provide insights into PPARγ activation by combining fluorine (19F) NMR and molecular dynamics simulations to characterize the nuclear receptor conformational ensemble in solution and the response of this ensemble to ligand and coregulatory peptide binding.

    • Ian M. Chrisman
    • , Michelle D. Nemetchek
    •  & Travis S. Hughes

  • Article
    | Open Access

    Mutations in superoxide dismutase-1 (SOD1) cause amyotrophic lateral sclerosis (ALS). Here the authors present the SOD1 crystal structure bound to the small cysteine-reactive molecule ebselen and show that ebselen is a chaperone for SOD1.

    • Michael J. Capper
    • , Gareth S. A. Wright
    •  & S. Samar Hasnain

  • Article
    | Open Access

    Membrane protein RodZ interacts with the actin-like protein MreB, which coordinates cell-wall insertion to maintain the typical rod-like shape of E. coli cells. Here, the authors provide evidence that RodZ modulates the biophysical properties of MreB and alters the spatial organization of cell-wall growth.

    • Alexandre Colavin
    • , Handuo Shi
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    The nucleolus is a membrane-less organelle formed through liquid–liquid phase separation (LLPS). Here the authors use biophysical methods and show that the nucleolar protein nucleophosmin (NPM1) also undergoes LLPS through homotypic, inter-NPM1 interactions and discuss implications for the ribosome biogenesis process.

    • Diana M. Mitrea
    • , Jaclyn A. Cika
    •  & Richard W. Kriwacki

  • Article
    | Open Access

    Src is a prototypical signaling non-receptor protein tyrosine kinase that interconverts between distinct conformations. Here the authors use variants of the kinase-inhibitor dasatinib to define three specific conformational states of the Src kinase and shed insight on the effect of conformation-specific inhibitors on Src dynamics.

    • Michael Tong
    • , Jeff G. Pelton
    •  & Markus A. Seeliger

  • Article
    | Open Access

    The spindle checkpoint ensures the fidelity of chromosome segregation during mitosis and meiosis. Here the authors use a combination of biochemical and structural biology approaches to show how the TRIP13 ATPase and its adaptor, p31comet, catalyze the conversion of the checkpoint protein Mad2 between latent and active forms

    • Melissa L. Brulotte
    • , Byung-Cheon Jeong
    •  & Xuelian Luo

  • Article
    | Open Access

    The disease causing L253P mutation in the actin-binding domain (ABD) of β-III-spectrin drastically increases actin-binding affinity. Here, the authors present the cryo-EM structure of F-actin complexed with the ABD mutant and double electron–electron resonance measurements show how the mutation affects the ABD conformational state.

    • Adam W. Avery
    • , Michael E. Fealey
    •  & Edward H. Egelman

  • Article
    | Open Access

    The proteasome regulates several important cellular processes and has been identified as a target for therapeutic interventions. Here the authors map the conformational and energy landscape of the 26S proteasome upon Oprozomib binding and uncover long-range allosteric effects that control the dynamic behaviour of the proteasome.

    • David Haselbach
    • , Jil Schrader
    •  & Holger Stark

  • Article
    | Open Access

    Allostery and drug-drug synergism can yield potential novel therapies with existing molecules. Here, the authors provide evidence that two unrelated drugs have increased cytotoxicity in cancer cells, which coincides with increased formation of chromatin adducts.

    • Zenita Adhireksan
    • , Giulia Palermo
    •  & Curt A. Davey

  • Article
    | Open Access

    Temperature differences between mosquitoes and humans trigger structural changes in dengue virus 2 (DENV2) particles, but not in other DENV serotypes. Here, using HDXMS, the authors describe serotype-specific expansion of intact viral particles of DENV1 and DENV2 at 28 °C (mosquitoes), 37 °C (humans) and 40 °C (fever).

    • Xin-Xiang Lim
    • , Arun Chandramohan
    •  & Ganesh S. Anand

  • Article
    | Open Access

    Eukaryotic RNA polymerase I (Pol I) is responsible for the transcription of rRNA genes. Here the authors determine the cryo-EM structure of the Pol I-Rrn3 complex, providing insight into how Rrn3 stabilizes the monomeric initiation competent Pol I to drive pre-initiation complex formation.

    • Michael Pilsl
    • , Corinne Crucifix
    •  & Patrick Schultz

  • Article
    | Open Access

    Aerolysin is a secreted bacterial pore forming toxin that inserts into the host plasma membrane, potentially leading to cell death. Here the authors present Cryo-EM structures of aerolysin arrested at different stages of the pore formation process that provide insight into the conformational changes that allow pore formation.

    • Ioan Iacovache
    • , Sacha De Carlo
    •  & Benoît Zuber

  • Article
    | Open Access

    When the antibiotic erythromycin is bound to the ribosomal exit tunnel, ErmBL peptide translation stalls and allows translation of the downstream methyltransferase ErmB. Here the authors combine cryo-EM and molecular dynamics simulations to identify the underlying basis for the inhibition of peptide bond formation that results in ribosome stalling.

    • Stefan Arenz
    • , Lars V. Bock
    •  & Daniel N. Wilson

  • Article
    | Open Access

    The activation of bacterial mechanosensitive channels is still not fully understood. Here, Bavi et al. show that the N-terminal helix of MscL dynamically couples membrane tension to channel gating, suggesting a conserved mechanism underlying the mechanosensitivity of ion channels of higher organisms.

    • Navid Bavi
    • , D. Marien Cortes
    •  & Boris Martinac

  • Article
    | Open Access

    Mutations in the extracellular domain of zinc transporter ZIP4 result in a lethal disorder. Here, the authors report the first crystal structure of ZIP4 extracellular domain, unveiling its unprecedented dimerization and two structural independent subdomains that have crucial roles in zinc transport.

    • Tuo Zhang
    • , Dexin Sui
    •  & Jian Hu

  • Article
    | Open Access

    The mechanism by which relaxin activates the relaxin family peptide receptor-1 is poorly understood. Here, Sethi et al.identify a relaxin binding site in an extracellular linker between the LDLa and LRR domains and propose that relaxin binding stabilizes a helical conformation that leads to receptor activation.

    • Ashish Sethi
    • , Shoni Bruell
    •  & Paul R. Gooley

  • Article
    | Open Access

    Mep2 proteins are tightly regulated fungal ammonium transporters. Here, the authors report the crystal structures of closed states of Mep2 proteins and propose a model for their regulation by comparing them with the open ammonium transporters of bacteria.

    • Bert van den Berg
    • , Anupama Chembath
    •  & Julian C. Rutherford

  • Article
    | Open Access

    Acetyl-CoA carboxylases are central regulatory hubs of fatty acid metabolism and are important targets for drug development in obesity and cancer. Here, the authors demonstrate that the regulation of these highly dynamic enzymes in fungi is governed by a mechanism based on phosphorylation-dependent conformational variability.

    • Moritz Hunkeler
    • , Edward Stuttfeld
    •  & Timm Maier

  • Article
    | Open Access

    Transient receptor potential (TRP) proteins are Ca2+-permeable cation channels activated by a range of chemical and physical stimuli. Here the authors describe a cryo-EM structure of the full-length TRPV2 channel that provides insight into the regulation of the TRPV subfamily of channels.

    • Kevin W. Huynh
    • , Matthew R. Cohen
    •  & Vera Y. Moiseenkova-Bell

  • Article
    | Open Access

    Single-molecule imaging of protein-DNA association requires fluorescently labelled protein, which limits the protein concentration that can be used. Here the authors exploit protein induced fluorescent enhancement of DNA sparsely labelled with Cy3 to visualize protein binding and correlate it with changes in DNA conformation.

    • Dan Song
    • , Thomas G. W. Graham
    •  & Joseph J. Loparo

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