scispace - formally typeset
Search or ask a question

Showing papers in "Journal of Structural Biology in 2012"


Journal ArticleDOI
TL;DR: Developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined are described.

4,554 citations


Journal ArticleDOI
TL;DR: Several modeling tools into UCSF Chimera include comparative modeling by MODELLER, simultaneous fitting of multiple components into electron microscopy density maps by IMP MultiFit, computing of small-angle X-ray scattering profiles and fitting of the corresponding experimental profile by IMP FoXS, and assessment of amino acid sidechain conformations based on rotamer probabilities and local interactions by Chimera.

499 citations


Journal ArticleDOI
TL;DR: This work studies the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series and shows how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.

368 citations


Journal ArticleDOI
TL;DR: Dynamo is a new software package for subtomogram averaging of cryo Electron Tomography (cryo-ET) data that allows user-transparent adaptation to a variety of high-performance computing platforms such as GPUs or CPU clusters and implements user-friendliness through GUI interfaces and scripting resources.

330 citations


Journal ArticleDOI
TL;DR: The open-source platform PyTom is introduced that unifies standard tomogram processing steps in a python toolbox and presents a novel stochastic classification method that yields significantly more accurate classification results than two deterministic approaches in simulations.

197 citations


Journal ArticleDOI
TL;DR: An automated procedure for the segmentation of actin filaments is described, which combines template matching with a new tracing algorithm, and the result is a set of lines, each one representing the central line of a filament.

185 citations


Journal ArticleDOI
TL;DR: Appraisal of the known structures and their classification uncovers a straightforward relationship between their architecture and the length of the repetitive units and this relationship and the repetitive character of structural folds suggest rules for better prediction of the 3D structures of such proteins.

179 citations


Journal ArticleDOI
TL;DR: These experiments indicate glyphosate induces cell membrane stiffening, and the appearance of cytoskeleton structures at a subcellular level, for low cytotoxic concentrations whereas cells exposed to IC50 (inhibitory concentration 50%) treatment exhibit control-like mechanical behavior despite obvious membrane damages.

151 citations


Journal ArticleDOI
TL;DR: Cryo X-ray tomography analysis reveals that about 70% of the host cell hemoglobin is taken up and digested during gametocyte development and the parasite eventually occupies about 50% of that in an uninfected erythrocyte volume.

150 citations


Journal ArticleDOI
TL;DR: A practical performance evaluation of a Direct Detection Device (DDD) for biological cryo-EM at two different microscope voltages shows that the DDD is capable of recording usable signal for 3D reconstructions at about 4/5 of the Nyquist frequency, which is a vast improvement over the performance of conventional imaging media.

147 citations


Journal ArticleDOI
TL;DR: The different biological functions of the shark teeth ("tearing" for Isurus and "cutting" for Galeocerdo) are controlled by the different geometry and not by the chemical or crystallographic composition.

Journal ArticleDOI
TL;DR: A completely novel method for EM specimen preparation based on small volume (picoliter to nanoliter) dispensing using inkjet technology is described and it is demonstrated that the piezo-electric inkjet mechanism does not disrupt the structural or functional integrity of macromolecules.

Journal ArticleDOI
TL;DR: The most recent mechanistic findings on yeast Hsp104 and Hsp70/Hsp40 cooperation in the remodeling of both types of aggregates are described, emphasizing similarities in the mechanism but also differences in the sensitivities towards chaperone activities.

Journal ArticleDOI
TL;DR: Current understanding of the conformational changes that ClpA or ClpX induce in ClpP to open the axial gate and increase substrate accessibility into the degradation chamber is reviewed.

Journal ArticleDOI
TL;DR: Cumulative evidence points to an important role for the lamina in regulating signaling and gene activity, and in mechanically coupling the cytoplasmic cytoskeleton to the nucleus.

Journal ArticleDOI
TL;DR: The automatic tracing together with a manual correction significantly reduces the amount of manual labor for tracing microtubules centerlines so that large-scale analysis of microtubule network properties becomes feasible.

Journal ArticleDOI
TL;DR: Ten methods for predicting protein-RNA interactions are reviewed, seven of which predict RNA-binding sites from protein sequences and three from structures, and a meta-predictor is developed that uses the output of top three sequence-basedPrimary predictors to calculate a consensus prediction, which outperforms all the primary predictors.

Journal ArticleDOI
TL;DR: It is demonstrated that robust and detailed super-resolution images of DNA can be produced by combining 5-ethynyl-2'-deoxyuridine (EdU) labeling using the 'click chemistry' approach and direct stochastic optical reconstruction microscopy (dSTORM).

Journal ArticleDOI
TL;DR: An incorporated fluorescence light microscope is developed which permits to record fluorescence, bright field and DIC images of cryogenic cells inside the TXM, and improves the spectral resolution by an order of magnitude.

Journal ArticleDOI
TL;DR: A new method for automatic alignment of projection images that does not require fiducial markers or manual interaction with the software is developed and gives users of the NCXT SXT instrument a new capability - virtually real-time initial 3D results during an imaging experiment, which can be further refined.

Journal ArticleDOI
TL;DR: The application of a recently established extension of the transmission soft X-ray cryo-microscope at the beamline U41-XM of the BESSY II electron storage ring is reported, demonstrating new possibilities to study the role of specific proteins in substructures of adherent cells, especially of the nucleus in toto, accessible to electron microscopy in thinned samples only.

Journal ArticleDOI
TL;DR: The open source software suite SIMPLE: Single-particle IMage Processing Linux Engine provides data analysis methods for single-particles cryo-electron microscopy by addressing the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations.

Journal ArticleDOI
TL;DR: Hard X-ray fluorescence microscopy and magnified phase contrast imaging are combined to obtain quantitative maps of the projected metal concentration in whole cells and absolute quantification at the sub-cellular level can be reached with the use of the proposed approach.

Journal ArticleDOI
TL;DR: Comparing the axonemal structure of three different organisms with widely divergent bending-motions by electron cryo-tomography defines the diversity of molecular architectures in these organisms, and forms the basis for future correlation with their different bending-Motions.

Journal ArticleDOI
TL;DR: This is the first X-ray crystal structure for a β-galactosidase used in food processing and it shows the tetrameric enzyme is a dimer of dimers, with higher dissociation energy for the dimers than for its assembly.

Journal ArticleDOI
TL;DR: Formin Cdc12p rejects actin subunits with a tag of ~2 kDa, illustrating the stringent structural requirements for this formin to promote the elongation of actin filament barbed ends as it moves processively along the end of a growing filament.

Journal ArticleDOI
TL;DR: This review aims to summarize the available data and discuss mechanistic models of the p97-cofactors' role in endosomal trafficking and autophagy, and finds that these pathways also deliver proteins for degradation, albeit by the lysosome.

Journal ArticleDOI
TL;DR: The studies on IF that have been carried out by the laboratory for more than 40 years are highlighted, based on conversations with Ueli Aebi which have taken place during adventurous and sometimes dangerous hiking and biking trips throughout the world.

Journal ArticleDOI
TL;DR: Development and studies have demonstrated the unique capabilities of multi-keV microscopy: namely, an ultra-low detection limit, large penetration depth, chemical sensitivity and three-dimensional imaging capabilities, and the capabilities have been extended towards sub-100nm lateral resolutions, thus enabling sub-cellular chemical imaging.

Journal ArticleDOI
TL;DR: X-ray micro-computed tomography and 3D printing elucidate the mechanism of conformational change from a passive (slightly curved, attached to surface) to a defensive (rolled, detached from surface) state of the plate assembly of T. marmorea, providing an understanding of how the chiton achieves the balance between mobility and protection.