Showing papers in "Journal of Structural Biology in 2016"

TL;DR: The main target of Gctf is to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra of observed micrographs after background subtraction to improve CTF parameters of all particles for subsequent image processing.

TL;DR: Scipion is a software framework for integrating several 3DEM software packages through a workflow-based approach that allows the execution of reusable, standardized, traceable and reproducible image-processing protocols.

TL;DR: Tests on the recently-published cryo-EM data of three complexes have demonstrated that the deep learning based scheme, DeepPicker, can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts.

TL;DR: A new device for preparing vitrified samples is presented, coupled to a new "self-blotting" grid that is developed to provide a method for spreading a sample to a thin film without the use of externally applied filter paper.

TL;DR: The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DN MT3s and explains the periodicity of de novo DNA methylation.

TL;DR: The canonical model of CME is examined, discrepancies with published experimental data are highlighted and future avenues of exploration are suggested while paying particular attention to the relationship between clathrin coated pits, plaques, sites of adhesion and the formation of endocytic 'hotspots'.

TL;DR: Comparisons of mechanical and electrical properties of all-gold supports to amorphous carbon foils show how the choice of support material and geometry can reduce specimen movement by more than an order of magnitude during low-dose imaging.

TL;DR: The efficacy of CWF is demonstrated by applying it to restore both simulated and experimental cryo-EM images and results with experimental datasets demonstrate that CWF provides a good way to evaluate the particle images and to see what the dataset contains even without 2D classification and averaging.

TL;DR: Nonclassical crystallization routes involving stable prenucleation clusters, dense liquid and solid amorphous precursor phases, as well as current nonclassical crystal growth models are described, which help to show that colloid-mediated crystal growth can be regarded as a wide-spread growth mechanism.

TL;DR: Large volume imaging using cryo FIB SEM, as demonstrated here, can contribute significantly to the understanding of the structures and functions of diverse biological tissues.

TL;DR: An algorithm called Iterative Compressed-sensing Optimized Non-uniform fast Fourier transform reconstruction (ICON) based on the theory of compressed-s sensing and the assumption of sparsity of biological specimens can significantly restore the missing information in comparison with other reconstruction algorithms.

TL;DR: This work presents a set of structure-relationship properties that are rooted in the nanogranular organization and proposes that they rest on a common pathway of formation, a colloid-driven and hence nonclassical mode of crystallization.

TL;DR: This work presents an extension of the original Pathwalking protocol, which can automatically trace a protein backbone directly from a near-atomic resolution (3-6Å) density map, and provides a more robust approach for backbone modeling.

TL;DR: The presence of surprisingly large amounts of mineral particles located inside membrane-delineated vesicles in the bone forming tissue between the blood vessels and the forming bone surface leads to the conclusion that important components of the bone mineralization pathways in rapidly forming chicken bone are dense phase mineral particles bound within membranes.

TL;DR: Interestingly, both of the catalytically-relevant conformations of this bacterial-like, low molecular weight TrxR in crystals are obtained without requiring an engineered disulfide linkage between Cys mutants of trxR and Trx (as was originally done with Escherichia coli Trx R and TrX).

TL;DR: This work investigates elastic and dissipative contributions from the primary load-bearing proteins in the distal region of byssal threads (the preCols) using X-ray diffraction (XRD) combined with in situ tensile testing and identifies cross β-sheet structure in the preCol flanking domains that functions as an elastic framework, providing hidden length.

TL;DR: X-ray crystal structure of Compound 6 complexed with HDAC8 is reported, and studies confirm that the HDACi induce the formation of and bind in theHDAC8-specific subpocket, offering insights into isoform-specific inhibition.

TL;DR: It is reported that coating the lipid-tail side of trehalose-embedded monolayer crystals with evaporated carbon appears to improve the consistency with which well-ordered, single crystals are observed to span over entire, 2μm holes of the support films.

TL;DR: In bacteria, the ability to remodel membrane underpins basic cell processes such as growth, and more sophisticated adaptations like intercell crosstalk, organelle specialisation, and pathogenesis.

TL;DR: Application of SAXS/WAXS provides valuable information on bone nanostructure and its constituents, effects of diseases and, prospectively, mechanical competence.

TL;DR: Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions.

TL;DR: Aβ42 fibrils contain a C-terminal β-arc-β motif with a special turn, termed "arc", at residues 37-38, which is absent in Aβ40 fibrillization, which can explain both the higher aggregation propensity of Aβ42 and the importance of A β42 to A β40 ratio in the pathogenesis of Alzheimer's disease.

TL;DR: A CTF correction algorithm for cryoSPT is developed without making any of the following assumptions, and speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2 are introduced.

TL;DR: Perception of the role that evo-devo can play within the field of biomineralogy is outlined, taking as a case study the past achievements, recent insights and some future research directions associated with gastropod shell formation.

TL;DR: An increase in available data makes it easier to compare skeletal repertoires, shedding light on the fundamental evolutionary mechanisms affecting matrix components, and a simple definition of the skeletal matrix is no longer possible.

TL;DR: This work has developed a simple cryo-FIB approach for thin frozen hydrated lamella fabrication, which fits both standard transmissioncryo-electron microscopes with side-entry Cryo-holders and state-of-the-art ones with AutoGrids.

TL;DR: It is suggested that the connection between the MamC-MIL structure and the protein's charged surfaces is crucial for magnetite binding and thus for the size control of the magnetite nanoparticles.

TL;DR: The combination of cryo-microscopy with elemental microanalysis and fluorescence imaging reveals new aspects of the biomineralization pathway in foraminifera which are, to date, unique in the world of biominERALization.

TL;DR: The crystal structure of USP7(CD123) is provided and it is shown that CD and Ubl123 are connected via an extended charged alpha helix and Mutational analysis is used to determine whether the charge and rigidity of this 'connector helix' are important for full USP6 activity.

TL;DR: This work forms an imaging model based on a Boltzmann transport equation, complemented by Monte Carlo simulations, and proposes to generalize the on-axis bright field detector to collect at angles well beyond the illumination cone to justify the generation of 3D images for micron thicknesses and beyond.