Showing papers in "Journal of Structural Biology in 2013"

TL;DR: The genetic identity of each virus particle present in the mixture can be assigned based solely on the structural information derived from single envelope glycoproteins displayed on the virus surface by the nuclear norm-based, collaborative alignment method presented here.

TL;DR: A space-frequency representation, the short-space Fourier transform, is proposed, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping, to improve the interpretability of reconstructions.

TL;DR: It is shown that Fourier ring correlation provides an easy-to-use, laboratory consistent standard for measuring the resolution of SRM images, and is provided a freely available software tool that combines resolution measurement with image reconstruction.

TL;DR: Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version, is presented, a central improvement is the concept of a project that stores the entire processing workflow from data import to final results.

TL;DR: An implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.

TL;DR: An easy-to-use software tool is developed, FindDQE, to measure MTF and DQE of electron detectors using images of a microscope's built-in beam stop, and compares the results from this method with published curves.

TL;DR: How recent in vitro models have addressed critical questions regarding the role of the non-collagenous proteins in controlling mineralization is discussed, the nature of the interactions between amorphous calcium phosphate and collagen during the early stages of mineralization, and therole of collagen in the mineralization process are discussed.

TL;DR: This novel approach will extend the currently available EM hybrid methods to the atomic-level interpretation of large conformational changes and their functional implications through the flexible fitting of atomic-resolution structures into electron microscopy (EM) density maps.

TL;DR: The use of cryo FIB-SEM is described as a tool for direct and fast 3D cryo-imaging of large native frozen samples including tissues.

TL;DR: Results, both experimental and computational, show that RRAR, RDAR, RPDR, RPRR and RPPR are capable of binding NRP-1, however, only RPPR and R PRR segments form an optimal organization around loop III with low potential energy.

TL;DR: A forward model that accounts for the specimen's scattering properties, microscope optics, and detector response and suggests that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected.

TL;DR: It is found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image and it also has little influence on high frequency signals.

TL;DR: A three-dimensional structural model of full-length talin is derived at a resolution of approximately 2.5nm using EM reconstruction ofFull- length talin and the known shapes of the individual domains and inter-domain angles as derived from small angle X-ray scattering.

TL;DR: This work crystallized Sirt2 in complex with a product analog, ADP-ribose, and solved this first crystal structure of a Sirt1-7 ligand complex at 2.3Å resolution, providing insights into the dynamics of the enzyme.

TL;DR: The observation that lacunar volume and morphology change over the human lifespan is novel, potentially resulting from preferential surface infilling within the extracellular space and likely impacts the mechanosensing function of the osteocyte network.

TL;DR: By optimizing data collection and defocus determination steps, this work has determined the structure of assembled Mason-Pfizer monkey virus Gag protein using sub-tomogram averaging to a resolution of 8.5 Å, demonstrating for the first time that high-resolution structural information can be obtained from cryo-electron tomogram averaging.

TL;DR: The presence of chitin in both marine (demosponges and hexactinellids and freshwater sponges indicates that this important structural biopolymer was already present in their common ancestor.

TL;DR: An efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics is proposed, which increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches.

TL;DR: The potential of cryo integrated light and electron microscopy is demonstrated for the detection of viable bacteria, the study of in vitro polymerized microtubules, the localization of mitochondria in mouse embryonic fibroblasts, and for a search into virus-induced intracellular membrane modifications within mammalian cells.

TL;DR: The results suggest that the BioEM framework can be used to analyze EM images of both ordered and disordered molecular systems, and offers an alternative to 3D-reconstruction methods, extracting accurate population distributions for highly flexible structures and their assemblies.

TL;DR: Evidence that trabecular bone parameters scale and correlate differently in rodents than in humans suggests that care should be applied when extrapolating bone biomechanical results from small animals to large-bodied humans.

TL;DR: Prisms in Pf and Pm are harder than in any other calcite prisms analyzed, their nanoparticles are smaller, and the angle spread is strongly correlated with hardness in all shells that form calcitic prismatic layers, the first structure-property relationship thus far hypothesized in mollusk shell prisms.

TL;DR: The study of Gα interacting surfaces in terms of sequence, structure and electrostatic potential reveals features that may account for the Gα subunit's behavior towards its interacting partners, suggesting electrostatic complementarity may be an important factor in G-protein interactions.

TL;DR: A new model showing how the mature tablet evolves from the primary colloidal ACC nanoparticles is proposed, which is expected to provide new insights into the formation of single crystal biominerals via the amorphous precursor route.

TL;DR: It is hypothesized that well developed/distinct "hoops" are compensatory adaptations in cases where increased osteon diameter is mechanically advantageous, and tested if there are correlations between osteon diameters and strongly hooped morphotypes in "tension", "compression", and "neutral axis" regions of femora (chimpanzees, humans), radii (horse, sheep) and calcanei ( horse, deer).

TL;DR: The swelling and shrinkage of four Picea abies (L. Karst) wood tissue homogeneous samples, of porosity varying between 45% and 78%, is documented with high-resolution synchrotron radiation phase-contrast X-ray tomographic microscopy and swelling anisotropy, in the tangential and radial directions, is found to increase with increasing porosity.

TL;DR: Though the cortex bone of rats is in part lamellar, its architecture is markedly different from that of the cortical bone of humans, a fact that must be borne in mind when using the rat as a model animal for studies of human bone biology and disease.

TL;DR: In this article, the nanostructure and nanomechanical properties of aggrecan monomers extracted and purified from human articular cartilage from donors of different ages (newborn, 29 and 38 year old) were directly visualized and quantified via atomic force microscopy (AFM)-based imaging and force spectroscopy.

TL;DR: A wide range of experiments show that the mineralization pathways proceed through a series of densification stages with intermediates, such as a "dense liquid" phase and the prenucleation clusters that form within it, consistent with the Gibbs concept of discontinuous phase transitions from supersaturated mother liquor to crystal.

TL;DR: A novel method for identifying the 3D locations of proteins using biotin-streptavidin labeling and cryo-electron tomography is reported, which is a powerful method to investigate the structure of large macromolecular complexes.