Journal: Journal of Structural Biology

Abbreviation

J Struct Biol

Publisher

Elsevier

Journal Volumes

ISSN

1047-8477
1095-8657

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Publications1 - 10 of 53
  • 3D imaging of microstructure of spruce wood
    Item type: Journal Article
    Trtik, P.; Dual, Jürg; Keunecke, D.; et al. (2007)
    Journal of Structural Biology
  • A set of common movements within GPCR-G-protein complexes from variability analysis of cryo-EM datasets
    Item type: Journal Article
    Marino, Jacopo; Schertler, Gebhard F.X. (2021)
    Journal of Structural Biology
    G-protein coupled receptors (GPCRs) are among the most versatile signal transducers in the cell. Once activated, GPCRs sample a large conformational space and couple to G-proteins to initiate distinct signaling pathways. The dynamical behavior of GPCR-G-protein complexes is difficult characterize structurally, and it might hinder obtaining routine high-resolution density maps in single-particle reconstructions. Here, we used variability analysis on the rhodopsin-Gi-Fab16 complex cryo-EM dataset, and the results provide insights into the dynamic nature of the receptor-complex interaction. We compare the outcome of this analysis with recent results obtained on the cannabinoid-Gi- and secretin-Gs-receptor complexes. Despite differences related to the biochemical compositions of the three samples, a set of consensus movements emerges. We anticipate that systematic variability analysis on GPCR-G-protein complexes may provide useful information not only at the biological level, but also for improving the preparation of more stable samples for cryo-EM single-particle analysis.
  • Direct transfer of electron microscopy samples to wetted carbon and graphene films via a support floatation block
    Item type: Journal Article
    de Martin Garrido, Natalia; Fu, Wencheng; Ramlaul, Kailash; et al. (2021)
    Journal of Structural Biology
    Support films are commonly used during cryo-EM specimen preparation to both immobilise the sample and minimise the exposure of particles at the air-water interface. Here we report preparation protocols for carbon and graphene supported single particle electron microscopy samples using a novel 3D-printed sample transfer block to facilitate the direct, wetted, movement of both carbon and graphene supports from the substrate on which they were generated to small volumes (10 μL) of sample. These approaches are simple and inexpensive to implement, minimise hydrophobic contamination of the support films, and are widely applicable to single particle studies. Our approach also allows the direct exchange of the sample buffer on the support film in cases in which it is unsuitable for vitrification, e.g. for samples from centrifugal density gradients that help to preserve sample integrity. © 2020 The Authors
  • AFM of biological material embedded in epoxy resin
    Item type: Journal Article
    Matsko, Nadezda; Mueller, Martin (2004)
    Journal of Structural Biology
  • Studying chaperone–proteases using a real-time approach based on FRET
    Item type: Journal Article
    Kolygo, Kristina; Ranjan, Namit; Kress, Wolfgang; et al. (2009)
    Journal of Structural Biology
  • Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase
    Item type: Journal Article
    Risser, Fanny; Collin, Sabrina; Dos Santos-Morais, Raphael; et al. (2020)
    Journal of Structural Biology
    Modular polyketide synthases (PKSs) are molecular-scale assembly lines comprising multiple gigantic polypeptide subunits. Faithful ordering of the subunits is mediated by extreme C- and N-terminal regions called docking domains (DDs). Decrypting how specificity is achieved by these elements is important both for understanding PKS function and modifying it to generate useful polyketide analogues for biological evaluation. Here we report the biophysical and structural characterisation of all six PKS/PKS interfaces in the unusual, chimaeric cis-AT/trans-AT PKS pathway responsible for biosynthesis of the antibiotic enacyloxin IIa in Burkholderia ambifaria. Taken together with previous work, our data reveal that specificity is achieved in the enacyloxin PKS by deploying at least three functionally orthogonal classes of DDs. We also demonstrate for the first time that cis-AT PKS subunits incorporate DDs with intrinsically disordered character, reinforcing the utility of such regions for achieving both medium affinity and high specificity at PKS intersubunit junctions. Overall, this work substantially increases the number of orthogonal DDs available for creating novel, highly-specific interfaces within cis- and trans-AT PKSs and their hybrids. It also reveals unexpected sequence/structure relationships in PKS DDs, identifying major current limitations to both accurately predicting and categorising these useful protein–protein interaction motifs. © 2020 Elsevier Inc.
  • Special issue: Biomolecular forces
    Item type: Other Journal Item
    Rief, Matthias; Müller, Daniel J. (2017)
    Journal of Structural Biology
  • Coalignment of osteocyte canaliculi and collagen fibers in human osteonal bone
    Item type: Journal Article
    Repp, Felix; Kollmannsberger, Philip; Roschger, Andreas; et al. (2017)
    Journal of Structural Biology
  • Inference of molecular structure for characterization and improvement of clinical grade immunocytokines
    Item type: Journal Article
    Ongaro, Tiziano; Guarino, Salvatore R.; Scietti, Luigi; et al. (2021)
    Journal of Structural Biology
    The use of immunomodulatory agents for the treatment of cancer is gaining a growing biopharmaceutical interest. Antibody-cytokine fusion proteins, namely immunocytokines, represent a promising solution for the regulation of the immune system at the site of disease. The three-dimensional arrangement of these molecules can profoundly influence their biological activity and pharmacokinetic properties. Structural techniques might provide important insight in the 3D arrangement of immunocytokines. Here, we performed structure investigations on clinical grade fusion proteins L19-IL2, IL12-L19L19 and L19L19-IL2 to elucidate their quaternary organization. Crystallographic characterization of the common L19 antibody fragment at a resolution of 2.0-Å was combined with low-resolution studies of the full-length chimeric molecules using small-angle synchrotron X-ray scattering (SAXS) and negative stain electron microscopy. Characterization of the full-length quaternary structures of the immunocytokines in solution by SAXS consistently supported the diabody structure in the L19-IL2 immunocytokine and allowed generation of low-resolution models of the chimeric proteins L19L19-IL2 and IL12-L19L19. Comparison with 3D reconstructions obtained from negative-stain electron microscopy revealed marked flexibility associated to the linker regions connecting the cytokine and the antibody components of the chimeric proteins. Collectively, our results indicate that low-resolution molecular structure characterizations provide useful complementary insights for the quality control of immunocytokines, constituting a powerful tool to guide the design and the subsequent optimization steps towards clinical enhancement of these chimeric protein reagents. © 2021 Elsevier
  • Reassessment of MxiH subunit orientation and fold within native Shigella T3SS needles using surface labelling and solid-state NMR
    Item type: Journal Article
    Verasdonck, Joeri; Shen, Da-Kang; Treadgold, Alexander; et al. (2015)
    Journal of Structural Biology
    T3SSs are essential virulence determinants of many Gram-negative bacteria, used to inject bacterial effectors of virulence into eukaryotic host cells. Their major extracellular portion, a ∼50 nm hollow, needle-like structure, is essential to host cell sensing and the conduit for effector secretion. It is formed of a small, conserved subunit arranged as a helical polymer. The structure of the subunit has been studied by electron cryomicroscopy within native polymers and by solid-state NMR in recombinant polymers, yielding two incompatible atomic models. To resolve this controversy, we re-examined the native polymer used for electron cryomicroscopy via surface labelling and solid-state NMR. Our data show the orientation and overall fold of the subunit within this polymer is as established by solid-state NMR for recombinant polymers.
Publications1 - 10 of 53