Nanocrystallography articles within Nature Communications

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  • Article
    | Open Access

    Here, the reaction of the suicide inhibitor sulbactam with the M. tuberculosis β-lactamase (BlaC) is investigated with time-resolved crystallography. Singular Value Decomposition is implemented to extract kinetic information despite changes in unit cell parameters during the time-course of the reaction.

    • Tek Narsingh Malla
    • , Kara Zielinski
    •  & Marius Schmidt

  • Article
    | Open Access

    An environmentally safe means of mosquito control is the application of Bacillus thuringiensis israelensis, which produces a cocktail of four naturally crystalline proteins exclusively toxic to mosquito. Here the authors report the atomic-resolution structures of Bti Cry11Aa and related Btj Cry11Ba solved de novo through Serial Femtosecond Crystallography on naturally-occurring nanocrystals.

    • Guillaume Tetreau
    • , Michael R. Sawaya
    •  & Jacques-Philippe Colletier

  • Article
    | Open Access

    DNA N6-adenine methylation (6 mA) plays a crucial role in epigenetic regulation in eukaryotes. Here, the authors determined nine crystal structures of the ciliates 6 mA methyltransferase complexes, providing the molecular basis for understanding the functions of 6 mA.

    • Jiyun Chen
    • , Rong Hu
    •  & Liang Liu

  • Article
    | Open Access

    There are a lack of tools to study the dynamics of (pseudo)hypohalous acids in live cells. Here the authors report a genetically encoded fluorescent biosensor, Hypocrates, for (pseudo)hypohalous acids and their derivatives which they use in cells and in a zebrafish tail fin injury model.

    • Alexander I. Kostyuk
    • , Maria-Armineh Tossounian
    •  & Vsevolod V. Belousov

  • Article
    | Open Access

    MAL and MyD88 are downstream adaptors of Toll-like receptors (TLR) and the MAL TIR domain forms filaments in vitro, which in turn nucleate the assembly of crystalline arrays of the MyD88 TIR domain. Here, the authors present the structure of these MyD88 TIR crystalline arrays solved by both microcrystal electron diffraction and serial femtosecond crystallography, and they show with mutagenesis experiments that MyD88 interface residues are important for TLR4 signaling in vivo.

    • Max T. B. Clabbers
    • , Susannah Holmes
    •  & Thomas Ve

  • Article
    | Open Access

    X-ray fee-electron lasers (XFELs) enable time-resolved crystallography experiments and the structure determination of proteins with little or no radiation damage. However currently it is unknown whether the designated 4.5 MHz maximum pulse rate for the European XFEL could lead to sample damage caused by shock waves from preceding pulses. Here, the authors address this question by performing a X-ray pump X-ray probe experiment on haemoglobin microcrystals at the Stanford XFEL facility that mimics the 4.5 MHz data collection mode and observe structural changes and a drop in diffraction data quality of the crystals.

    • Marie Luise Grünbein
    • , Alexander Gorel
    •  & Ilme Schlichting

  • Article
    | Open Access

    The viral Protein Kinase-1 (PK-1) phosphorylates the regulatory protein p6.9, which facilitates baculoviral genome release. Here, the authors combine X-ray crystallography with biophysical and biochemical analyses as well as molecular dynamics simulations to characterize Cydia pomenella granulovirus PK-1, which forms a dimer with a parallel side-to-side arrangement of the kinase domains and furthermore, they provide insights into its catalytic mechanism and evolutionary relationships with other kinases.

    • Michael R. Oliver
    • , Christopher R. Horne
    •  & James M. Murphy

  • Article
    | Open Access

    The SARS-CoV-2 papain-like protease (PLpro) is of interest as a drug target. Here, the authors identify GRL0617 as a PPI (protein–protein interaction) inhibitor of SARS-CoV-2 PLpro that inhibits its deISGylating activity and present the mechanism of action of the compound through the GRL0617-bound PLpro crystal structure and NMR studies.

    • Ziyang Fu
    • , Bin Huang
    •  & Hao Huang

  • Article
    | Open Access

    Rhodopsin phosphodiesterase (Rh-PDE) hydrolyzes both cAMP and cGMP in a light-dependent manner. Structural and functional analyses of the Rh-PDE from Salpingoeca rosetta reveal unusual rhodopsin topology comprising 8 transmembrane helices (TMs) and suggest that TM0 plays a crucial role in the enzymatic photoactivity.

    • Tatsuya Ikuta
    • , Wataru Shihoya
    •  & Osamu Nureki

  • Article
    | Open Access

    Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.

    • Dennis Della Corte
    • , Hugo L. van Beek
    •  & Jan Marienhagen

  • Article
    | Open Access

    Due to the pulsed nature of X-ray free electron laser (XFEL) instruments the majority of protein crystals, which are injected using continuous jet injection techniques are wasted. Here, the authors present a microfluidic device to deliver aqueous protein crystal laden droplets segmented with an immiscible oil and demonstrate that with this device an approx. 60% reduction in sample waste was achieved for data collection of 3-deoxy-D-manno-octulosonate 8-phosphate synthase crystals at the EuXFEL.

    • Austin Echelmeier
    • , Jorvani Cruz Villarreal
    •  & Alexandra Ros

  • Article
    | Open Access

    The local X-ray-induced dynamics that occur in protein crystals during serial femtosecond crystallography (SFX) measurements at XFELs are not well understood. Here the authors performed a time-resolved X-ray pump X-ray probe SFX experiment, and they observe distinct structural changes in the disulfide bridges and peptide backbone of proteins; complementing theoretical approaches allow them to further characterize the details of the X-ray induced ionization and local structural dynamics.

    • Karol Nass
    • , Alexander Gorel
    •  & Ilme Schlichting

  • Article
    | Open Access

    Bacillus thuringiensis israelensis (Bti) produces the naturally-crystalline proteinaceous toxin Cyt1Aa that is toxic to mosquito larvae. Here the authors grow recombinant nanocrystals of the Cyt1Aa protoxin in vivo and use serial femtosecond crystallography to determine its structure at different redox and pH conditions and by combining their structural data with further biochemical, toxicological and biophysical analyses provide mechanistic insights into the Cyt1Aa bioactivation cascade.

    • Guillaume Tetreau
    • , Anne-Sophie Banneville
    •  & Jacques-Philippe Colletier

  • Article
    | Open Access

    For conventional three-dimensional microcrystal electron diffraction (3D ED/MicroED), a crystal is slowly rotated under an electron beam, leading to inevitable accumulation of radiation damage during data collection. In this work, the authors present a serial electron diffraction method, where still diffraction patterns from many protein nanocrystals are rapidly recorded and merged, which minimises radiation damage and only requires a slightly modified standard scanning transmission electron microscope.

    • Robert Bücker
    • , Pascal Hogan-Lamarre
    •  & R. J. Dwayne Miller

  • Article
    | Open Access

    rsEGFP2 is a reversibly photoswitchable fluorescent protein used in super-resolution light microscopy. Here the authors present the structure of an rsEGFP2 ground-state intermediate after excited state-decay that was obtained by nanosecond time-resolved serial femtosecond crystallography at an X-ray free electron laser, and time-resolved absorption spectroscopy measurements complement their structural analysis.

    • Joyce Woodhouse
    • , Gabriela Nass Kovacs
    •  & Martin Weik

  • Article
    | Open Access

    The European X-ray free-electron laser (EuXFEL) in Hamburg is the first XFEL with a megahertz repetition rate. Here the authors present the 2.9 Å structure of the large membrane protein complex Photosystem I from T. elongatus that was determined at the EuXFEL.

    • Chris Gisriel
    • , Jesse Coe
    •  & Nadia A. Zatsepin

  • Article
    | Open Access

    Bacteriorhodopsin (bR) is a light-driven proton pump. Here the authors combine time-resolved crystallography at a free-electron laser, ultrafast spectroscopy and quantum chemistry to study the structural changes following multiphoton photoexcitation of bR and find that they occur within 300 fs not only in the light-absorbing chromophore but also in the surrounding protein.

    • Gabriela Nass Kovacs
    • , Jacques-Philippe Colletier
    •  & Ilme Schlichting

  • Article
    | Open Access

    The new European X-Ray Free-Electron Laser (EuXFEL) is the first XFEL that generates X-ray pulses with a megahertz inter-pulse spacing. Here the authors demonstrate that high-quality and damage-free protein structures can be obtained with the currently available 1.1 MHz repetition rate pulses using lysozyme as a test case and furthermore present a β-lactamase structure.

    • Max O. Wiedorn
    • , Dominik Oberthür
    •  & Anton Barty

  • Article
    | Open Access

    The European X-ray free-electron laser (EuXFEL) in Hamburg is the first megahertz (MHz) repetition rate XFEL. Here the authors use lysozyme crystals and microcrystals from jack bean proteins and demonstrate that damage-free high quality data can be collected at a MHz repetition rate.

    • Marie Luise Grünbein
    • , Johan Bielecki
    •  & Ilme Schlichting

  • Article
    | Open Access

    The transient receptor potential channel TRPV6 mediates calcium uptake in epithelia and its expression is increased in several cancer types. Here, authors present structures of TRPV6 bound to 2-APB, a TRPV6 inhibitor, and show that 2-APB induces TRPV6 channel closure by modulating protein–lipid interactions.

    • Appu K. Singh
    • , Kei Saotome
    •  & Alexander I. Sobolevsky

  • Article
    | Open Access

    Jumonji-C domain containing protein 5 (JMJD5) is essential for animal development but its catalytic activity has remained elusive so far. Here the authors show that human JMJD5 is an arginyl-hydroxylase and present the cofactor, substrate and product bound JMJD5 crystal structures.

    • Sarah E. Wilkins
    • , Md. Saiful Islam
    •  & Rasheduzzaman Chowdhury

  • Article
    | Open Access

    The first step in bacterial phospholipid biosynthesis is the acylation of glycerol 3-phosphate to form lysophosphatidic acid. Here, the authors present the high resolution crystal structure of the glycerol 3-phosphate acyltransferase PlsY, a membrane protein and give insights into its catalytical mechanism.

    • Zhenjian Li
    • , Yannan Tang
    •  & Dianfan Li

  • Article
    | Open Access

    X-ray free-electron lasers produce bright femtosecond X-ray pulses. Here, the authors use a two-colour X-ray free-electron laser beam for simultaneous two-wavelength data collection and show that protein structures can be determined with multiple wavelength anomalous dispersion phasing, which is important for difficult-to-phase projects.

    • Alexander Gorel
    • , Koji Motomura
    •  & Ilme Schlichting

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