PubMed Journal Database | Journal of structural biology 
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Showing PubMed Articles 1–25 of 33 from Journal of structural biology
Vitreous cryo-section-induced compression influences the interpretation and the reliability of electron microscopy images and tomographic reconstructions. Previous studies of this deformation have been focused at the cellular level where considerable compression occurs, yet the degree of possible intracellular macromolecular deformation has remained unclear. Here, electron cryo-tomographic reconstructions of vitreous cryo-sections show that 80S ribosomes, both intracellular and in an isolated state, appear...
Matching Structural Densities from Different Biophysical Origins with Gain and Bias.
The registration of volumetric structures in real space involves geometric and density transformations that align a target map and a probe map in the best way possible. Many computational docking strategies exist for finding the geometric transformations that superimpose maps, but the problem of finding an optimal density transformation, for the purposes of difference calculations or segmentation, has received little attention in the literature. We report results based on simulated and experimental electron...
Conformational Dynamics of Supramolecular Protein Assemblies.
Supramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into...
Crystal structure of a dimeric archaeal Cleavage and Polyadenylation Specificity Factor.
Proteins of the metallo-β-lactamase (MβL) fold form a large superfamily of metallo-hydrolase/oxidoreductases. Members of this family are found in all three domains of life and are involved in a variety of biological functions related to hydrolysis, redox processes, DNA repair and uptake, and RNA processing. We classified the archaeal homologs of this superfamily based on sequence similarity and characterized a subfamily of the Cleavage and Polyadenylation Specificity Factor (CPSF) with an uncommon domain...
Focal Issue on Hybrid Imaging.
Three-dimensional molecular modeling with single molecule FRET.
Single molecule fluorescence energy transfer experiments enable investigations of macromolecular conformation and folding by the introduction of fluorescent dyes at specific sites in the macromolecule. Multiple such experiments can be performed with different labeling site combinations in order to map complex conformational changes or interactions between multiple molecules. Distances that are derived from such experiments can be used for determination of the fluorophore positions by triangulation. When com...
The calculation of projection structures (PSs) from Protein Data Bank (PDB)-coordinate files of membrane proteins is not well-established. Reports on such attempts exist but are rare. In addition, the different procedures are barely described and thus difficult if not impossible to reproduce. Here we present a simple, fast and well-documented method for the calculation and visualization of PSs from PDB-coordinate files of membrane protein: the projection structure visualization (PSV)-method. The PSV-method...
The Structure of a COPII Tubule.
Nearly a third of all eukaryotic proteins are transported from the ER to the Golgi apparatus through the secretory pathway using COPII coated vesicles. Evidence suggests that this transport occurs via 500-900 Å vesicles that bud from the ER membrane. It has been shown that procollagen molecules utilize the COPII proteins for transport, but it is unclear how the COPII coat can accommodate these ∼3,000 Å long molecules. We now present a cryogenic electron tomographic reconstruction of a Sec13/31 tubule th...
Central to protein architecture is the local arrangement or secondary structure of the polypeptide backbone. Thirty to forty percent of protein domains are α-helices with 3.6 residues per turn. Π-Helices, in which the peptide chain is more loosely coiled (4.4 residues per turn), have also been proposed. However, such structures necessitate an energetically unfavorable ∼1Å central helical hole. We show that rather than being composed of idealized Π-helices, helical regions formed from putative Π-helic...
Hysteretic swelling of wood at cellular scale probed by phase contrast X-ray tomography.
We investigated the three-dimensional, microscopic, dimensional changes of Picea abies (L. Karst) wood samples due to controlled steps of the ambient relative humidity. The study was performed at the wood cellular scale by high resolution synchroton radiation phase-contrast X-ray tomographic microscopy (srPCXTM). Tomographic images were taken after the samples achieved moisture equilibrium at five adsorption and four desorption steps. For spruce latewood, swelling and shrinkage are found to be larger, more...
Native architecture of the photosynthetic membrane from Rhodobacter veldkampii.
The photosynthetic membrane in purple bacteria contains several pigment-protein complexes that assure light capture and establishment of the chemiosmotic gradient. The bioenergetic tasks of the photosynthetic membrane require the strong interaction between these various complexes. In the present work, we acquired the first images of the native outer membrane architecture and the supramolecular organization of the photosynthetic apparatus in vesicular chromatophores of Rhodobacter (Rb.) veldkampii. Mixed wit...
Arrangement of trichokeratin intermediate filaments and matrix in the cortex of Merino wool.
Tomograms of transverse sections of Merino wool fibers obtained from fleeces differing in fiber curvature were reconstructed from image series collected using a 300kV transmission electron microscope. Trichokeratin intermediate filaments (IFs) from the ortho-, para- and mesocortices were modeled from the tomograms. IFs were predominantly arranged in left-handed concentric helices with the relative angle of IFs increasing progressively from the center to the periphery of orthocortex macrofibrils. The median...
Superoxide dismutases (SODs) are metalloenzymes catalysing the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Here, we present the crystal structure of a cold-adapted Fe-SOD from the Antarctic eubacterium Pseudoalteromonas haloplanktis (PhSOD), and that of its complex with sodium azide. The structures were compared with those of the corresponding homologues having a high sequence identity with PhSOD, such as the mesophilic SOD from Escherichia coli (EcSOD) or Pseudomon...
The aromatized chromophore (Chr) of C-1027 with selective DNA-cleaving ability, which is stabilized and delivered by the apoprotein (Apo) in vitro, is not released until the holoprotein (Apo + Chr) penetrates into the cultured cancer cells. As a drug delivery system, the holoprotein has gained much attention in clinical application. However, the Chr-releasing mechanism is ambiguous so far. In this paper, the releasing pathway is investigated using conventional molecular dynamics (MD), essential dynamics (ED...
Direct observation of subcellular structures and their characterization is essential for understanding their physiological functions. To observe them in open environment, we have developed an inverted scanning electron microscope with a detachable, open-culture dish, capable of 8nm resolution, and combined with a fluorescence microscope quasi-simultaneously observing the same area from the top. For scanning electron microscopy from the bottom, a silicon nitride film window in the base of the dish maintains...
Maximum Likelihood based Classification of Electron Tomographic Data.
Classification and averaging of sub-tomograms can improve the fidelity and resolution of structures obtained by electron tomography. Here we present a three-dimensional (3D) Maximum Likelihood algorithm - MLTOMO - which is characterized by integrating 3D alignment and classification into a single, unified processing step. The novelty of our approach lies in the way we calculate the probability of observing an individual sub-tomogram for a given reference structure. We assume that the reference structure is...
Vibrio alginolyticus use flagella to swim. A flagellum consists of a filament, hook and basal body. The basal body is made up of a rod and several ring structures. This study investigates the structure of the T ring which is a unique component of the V. alginolyticus sodium ion-driven flagellar basal body. Using Zernike phase contrast (ZPC) cryo-electron tomography, we compared the 3D structures of purified hook-basal bodies (HBB) from a wild-type strain (KK148) and a deletion mutant lacking motX and motY (...
The interstitial green sheets in abalone shell nacre are shown to be bifacially differentiated trilaminate polymeric complexes, with glycoprotein layers sandwiching a central core containing chitin. They share some common feature with the organic matrix layers between the aragonite tablets in the nacre and the periostracum, and show similarities to the myostracum. Thus, although the green sheet is reported to be unique to the abalone shell, it represents an interesting model for the study of molluscan shell...
Bone has a complex hierarchical structure that has evolved to serve structural and metabolic roles in the body. Due to the complexity of bone structure and the number of diseases which affect the ultrastructural constituents of bone, it is important to develop quantitative methods to assess bone nanoscale properties. Autosomal dominant Osteogenesis Imperfecta results predominantly from glycine substitutions (80%) and splice site mutations (20%) in the genes encoding the alpha1 or alpha2 chains of Type I col...
Existing protein structure classifications group proteins by overall structural similarity at the highest level and by evolutionary relationships at the lowest level, deriving higher-level groups by pairwise structure comparison. For this to be successful requires that large changes in structure are relatively rare in evolution and that proteins with no detectable evolutionary relationship do not converge on similar global chain conformations since this creates conflicts between structural and evolutionary...
We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T 7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently...
Molecular dynamics simulations of the wild type bovine ADP/ATP mitochondrial carrier, and of the single Ala113Pro and double Ala113Pro/Val180Met mutants, embedded in a lipid bilayer, have been carried out for 30 ns to shed light on the structural-dynamical changes induced by the Val180Met mutation restoring the carrier function in the Ala113Pro pathologic mutant. Principal component analysis indicates that, for the three systems, the protein dynamics is mainly characterized by the motion of the matrix loops...
beta-Glucosidases (EC 3.2.1.21) cleave beta-glucosidic linkages in disaccharide or glucose-substituted molecules and play important roles in fundamental biological processes. beta-Glucosidases have been widely used in agricultural, biotechnological, industrial and medical applications. In this study, a high yield expression (70-250 mg/l) in Escherichia coli of the three functional beta-glucosidase genes was obtained from the bacterium Clostridium cellulovorans (CcBglA), the fungus Trichoderma reesei (TrBgl2...
In general, plant cell wall degrading enzymes are modular proteins containing catalytic domains linked to one or more non catalytic Carbohydrate-Binding Modules (CBMs). Xyn10B from Clostridium thermocellum is a typical modular enzyme containing an N-terminal family 22 CBM (CBM22-1), a family 10 Glycoside Hydrolase catalytic domain (GH10), a second CBM22 (CBM22-2), a dockerin sequence and a C-terminal family 1 Carbohydrate Esterase (CE1) catalytic domain. The structure of the N-terminal bi-modular CBM22-1-GH...
NMR characterization of foldedness for the production of E3 RING domains.
We summarize the use of NMR spectroscopy in the production and the screening of stability and foldedness of protein domains, and apply it to the RING domains of E3 ubiquitin-ligases. RING domains are involved in specific interactions with E2 ubiquitin conjugating enzymes and thus play an essential role in the ubiquitination pathway. Protein production of the Zn(2+) containing and cysteine rich RING domains for molecular studies frequently turns out to be problematic. We compared the expression and solubilit...
