abstract：:CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm whi...

journal_title：Journal of structural biology

authors： Rohou A,Grigorieff N

更新日期：2015-11-01 00:00:00

abstract：:While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally tr...

journal_title：Journal of structural biology

authors： Sarre A,Ökvist M,Klar T,Hall DR,Smalås AO,McSweeney S,Timmins J,Moe E

更新日期：2015-08-01 00:00:00

abstract：:The hyaluronate receptor CD44 plays role in cell adhesion and migration and is involved in tumor metastasis. The extracellular domain of CD44 comprises the hyaluronate-binding domain (HABD) and the membrane-proximal stem region; the short intracellular portion interacts with adaptor proteins and triggers signaling pat...

journal_title：Journal of structural biology

authors： Škerlová J,Král V,Kachala M,Fábry M,Bumba L,Svergun DI,Tošner Z,Veverka V,Řezáčová P

更新日期：2015-08-01 00:00:00

abstract：:The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damag...

journal_title：Journal of structural biology

authors： Diebolder CA,Faas FG,Koster AJ,Koning RI

更新日期：2015-05-01 00:00:00

abstract：:The molecular mechanism underlining the antibacterial activity of the bacteriocin AS-48 is not known, and two different and opposite alternatives have been proposed. Available data suggested that the interaction of positively charged amino acids of AS-48 with the membrane would produce membrane destabilization and dis...

journal_title：Journal of structural biology

authors： Cebrián R,Martínez-Bueno M,Valdivia E,Albert A,Maqueda M,Sánchez-Barrena MJ

更新日期：2015-05-01 00:00:00

abstract：:In arthropods the cuticle forms an exoskeleton with its physical and chemical properties adapted to functions of distinct skeletal elements. The cuticle of the partes incisivae (PI) in mandibles of terrestrial isopods is a composite of chitin-protein fibrils/fibres and minerals. It consists of an unmineralized tip, a ...

journal_title：Journal of structural biology

authors： Huber J,Griesshaber E,Nindiyasari F,Schmahl WW,Ziegler A

更新日期：2015-05-01 00:00:00

abstract：:Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative proc...

journal_title：Journal of structural biology

authors： Sorzano CO,Vargas J,de la Rosa-Trevín JM,Otón J,Álvarez-Cabrera AL,Abrishami V,Sesmero E,Marabini R,Carazo JM

更新日期：2015-03-01 00:00:00

abstract：:Nonlinear optical processes have found widespread applications in fields ranging from fundamental physics to biomedicine. In this study, we attempted to evaluate cell activation by using the Third Harmonic Generation (THG) imaging microscopy as a new diagnostic tool. The BV-2 microglia cell line with or without activa...

journal_title：Journal of structural biology

authors： Gavgiotaki E,Filippidis G,Kalognomou M,Tsouko AA,Skordos I,Fotakis C,Athanassakis I

更新日期：2015-02-01 00:00:00

abstract：:Tomo3D is a program for fast tomographic reconstruction on multicore computers. Its high speed stems from code optimization, vectorization with Streaming SIMD Extensions (SSE), multithreading and optimization of disk access. Recently, Advanced Vector eXtensions (AVX) have been introduced in the x86 processor architect...

journal_title：Journal of structural biology

authors： Agulleiro JI,Fernandez JJ

更新日期：2015-02-01 00:00:00

abstract：:The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP) is one of the most commonly available over-the-counter pharmaceutic...

journal_title：Journal of structural biology

authors： Orlando BJ,Lucido MJ,Malkowski MG

更新日期：2015-01-01 00:00:00

abstract：:Ion mobility mass spectrometry was employed to study the structure of the βB2B3-crystallin heterodimer following oxidation through its increased exposure to hydroxyl radicals. The results demonstrate that the heterodimer can withstand limited oxidation through the incorporation of up to some 10 oxygen atoms per subuni...

journal_title：Journal of structural biology

authors： Akashi S,Maleknia SD,Saikusa K,Downard KM

更新日期：2015-01-01 00:00:00

abstract：:A new era has begun for single particle cryo-electron microscopy (cryoEM) which can now compete with X-ray crystallography for determination of protein structures. The development of direct detectors constitutes a revolution that has led to a wave of near-atomic resolution cryoEM reconstructions. However, regardless o...

journal_title：Journal of structural biology

authors： Campbell MG,Kearney BM,Cheng A,Potter CS,Johnson JE,Carragher B,Veesler D

更新日期：2014-11-01 00:00:00

abstract：:Substrate binding to enzymes often follows a precise order where catalysis is accomplished through programmed conformational changes. Short-chain dehydrogenase/reductase (SDR) enzymes follow sequential order 'bi-bi' reaction kinetics. The mechanistic study of a SDR homolog, reductase (R) domain, from multifunctional e...

journal_title：Journal of structural biology

authors： Haque AS,Patel KD,Deshmukh MV,Chhabra A,Gokhale RS,Sankaranarayanan R

更新日期：2014-09-01 00:00:00

abstract：:The crystal structure of the N-terminal domain of the RNA polymerase δ subunit (Nδ) from Bacillus subtilis solved at a resolution of 2.0Å is compared with the NMR structure determined previously. The molecule crystallizes in the space group C222(1) with a dimer in the asymmetric unit. Importantly, the X-ray structure ...

journal_title：Journal of structural biology

authors： Demo G,Papoušková V,Komárek J,Kadeřávek P,Otrusinová O,Srb P,Rabatinová A,Krásný L,Žídek L,Sklenář V,Wimmerová M

更新日期：2014-08-01 00:00:00

abstract：:Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to stu...

journal_title：Journal of structural biology

authors： Yu G,Vago F,Zhang D,Snyder JE,Yan R,Zhang C,Benjamin C,Jiang X,Kuhn RJ,Serwer P,Thompson DH,Jiang W

更新日期：2014-07-01 00:00:00

abstract：:The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix...

journal_title：Journal of structural biology

authors： Kükenshöner T,Wohlwend D,Niemöller C,Dondapati P,Speck J,Adeniran AV,Nieth A,Gerhardt S,Einsle O,Müller KM,Arndt KM

更新日期：2014-06-01 00:00:00

abstract：:The repetitive Gly-X-Y sequence is the telltale sign of triple helical domains in collagens and collagen-like proteins. Most collagen sequences contain sporadic interruptions of this pattern, which may have functional roles in molecular flexibility, assembly or molecular recognition. However, the structural signatures...

journal_title：Journal of structural biology

authors： Bella J

更新日期：2014-06-01 00:00:00

abstract：:Infection of plants by Zucchini Yellow Mosaic Virus (ZYMV) induces severe ultrastructural changes. The aim of this study was to investigate ultrastructural changes during ZYMV-infection in Cucurbita pepo L. plants on the two and three dimensional (2D and 3D) level and to correlate these changes with the spread of ZYMV...

journal_title：Journal of structural biology

authors： Zellnig G,Pöckl MH,Möstl S,Zechmann B

更新日期：2014-05-01 00:00:00

abstract：:The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution ...

journal_title：Journal of structural biology

authors： Rohou A,Grigorieff N

更新日期：2014-05-01 00:00:00

abstract：:The carboxy-terminal region of the KCNH family of potassium channels contains a cyclic-nucleotide binding homology domain (CNBHD) that is important for channel gating and trafficking. The solution structure of the CNBHD of the KCNH potassium of zebrafish was determined using solution NMR spectroscopy. This domain exis...

journal_title：Journal of structural biology

authors： Li Q,Ng HQ,Yoon HS,Kang C

更新日期：2014-04-01 00:00:00

abstract：:The C1q-tumor necrosis factor 5 (C1QTNF5) protein plays a significant role in retinal pigmented epithelium (RPE) cellular adhesion. The C1QTNF5 gene is co-transcribed with the frizzled-related protein (MFRP) gene. A Ser-to-Arg mutation at site 163 (S163R) in C1QTNF5 is known to cause late-onset retinal macular degener...

journal_title：Journal of structural biology

authors： Tu X,Palczewski K

更新日期：2014-04-01 00:00:00

abstract：:Random spherically constrained (RSC) single particle reconstruction is a method to obtain structures of membrane proteins embedded in lipid vesicles (liposomes). As in all single-particle cryo-EM methods, structure determination is greatly aided by reliable detection of protein "particles" in micrographs. After fittin...

journal_title：Journal of structural biology

authors： Liu Y,Sigworth FJ

更新日期：2014-03-01 00:00:00

abstract：:Net-negatively-charged heterospecific A:B:C collagen peptide heterotrimers were designed using an automated computational approach. The design algorithm considers both target stability and the energy gap between the target states and misfolded competing states. Structural characterization indicates the net-negative ch...

journal_title：Journal of structural biology

authors： Parmar AS,Zahid S,Belure SV,Young R,Hasan N,Nanda V

更新日期：2014-02-01 00:00:00

abstract：:Integration of fluorescence light and transmission electron microscopy into the same device would represent an important advance in correlative microscopy, which traditionally involves two separate microscopes for imaging. To achieve such integration, the primary technical challenge that must be solved regards how to ...

journal_title：Journal of structural biology

authors： Iijima H,Fukuda Y,Arai Y,Terakawa S,Yamamoto N,Nagayama K

更新日期：2014-01-01 00:00:00

abstract：:Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challeng...

journal_title：Journal of structural biology

authors： Guerrero-Ferreira RC,Wright ER

更新日期：2014-01-01 00:00:00

abstract：:The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization ...

journal_title：Journal of structural biology

authors： Dietlmeier J,Ghita O,Duessmann H,Prehn JH,Whelan PF

更新日期：2013-12-01 00:00:00

abstract：:Nacre is the iridescent inner lining of many mollusk shells, with a unique lamellar structure at the sub-micron scale, and remarkable resistance to fracture. Despite extensive studies, nacre formation mechanisms remain incompletely understood. Here we present 20-nm, 2°-resolution polarization-dependent imaging contras...

journal_title：Journal of structural biology

authors： Olson IC,Blonsky AZ,Tamura N,Kunz M,Pokroy B,Romao CP,White MA,Gilbert PU

更新日期：2013-12-01 00:00:00

abstract：:The human vertebral body and intervertebral disc interface forms the region where the cartilaginous endplate, annulus fibrosis and bone of the vertebral body are connected through an intermediate calcified cartilage layer. While properties of both the vertebral body and components of the disc have been extensively stu...

journal_title：Journal of structural biology

authors： Paietta RC,Burger EL,Ferguson VL

更新日期：2013-11-01 00:00:00

abstract：:The first step to understanding brain function is to determine the brain's network structure. We report a three-dimensional analysis of the brain network of the fruit fly Drosophila melanogaster by synchrotron-radiation tomographic microscopy. A skeletonized wire model of the left half of the brain network was built b...

journal_title：Journal of structural biology

authors： Mizutani R,Saiga R,Takeuchi A,Uesugi K,Suzuki Y

更新日期：2013-11-01 00:00:00

abstract：:The actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric...

journal_title：Journal of structural biology

authors： Gayathri P,Fujii T,Namba K,Löwe J

更新日期：2013-10-01 00:00:00

abstract：:Rlf is a guanine nucleotide exchange factor for the small G-proteins RalA and RalB and couples Ras- to Ral-signalling. Here the crystal structure of the catalytic module of Rlf consisting of a REM- and a CDC25-homology domain is determined. The structure is distinguished by an extended three stranded β-sheet called th...

journal_title：Journal of structural biology

authors： Popovic M,Jakobi AJ,Rensen-de Leeuw M,Rehmann H

更新日期：2013-09-01 00:00:00

abstract：:With the development of Cryo Electron Microscopy Of Vitreous Sections (CEMOVIS), imaging cells in a close to native state has become a reality. However with the commonly used carriers for high-pressure freezing and cryo-sectioning, adherent grown cells either need to be detached from their substrate. Here a new method...

journal_title：Journal of structural biology

authors： Mesman RJ

更新日期：2013-09-01 00:00:00

abstract：:For the understanding of mineral formation processes from solution it is important to obtain a deeper insight into the dynamics of crystal growth. In this study we applied for this purpose a novel atmospheric scanning electron microscope that allows the investigation of CaCO3 particle formation in solution under atmos...

journal_title：Journal of structural biology

authors： Verch A,Morrison IE,Locht Rv,Kröger R

更新日期：2013-08-01 00:00:00

abstract：:Aminoglycoside 4-phosphotransferase-Ia (APH(4)-Ia)/Hygromycin B phosphotransferase (Hph) inactivates the aminoglycoside antibiotic hygromycin B (hygB) via phosphorylation. The crystal structure of the binary complex of APH(4)-Ia with hygB was recently reported. To characterize substrate recognition by the enzyme, we d...

journal_title：Journal of structural biology

authors： Iino D,Takakura Y,Fukano K,Sasaki Y,Hoshino T,Ohsawa K,Nakamura A,Yajima S

更新日期：2013-07-01 00:00:00

abstract：:Cystathionine β-synthase (CBS) domains are small intracellular modules that can act as binding domains for adenosine derivatives, and they may regulate the activity of associated enzymes or other functional domains. Among these, the single CBS domain-containing proteins, CBSXs, from Arabidopsis thaliana, have recently...

journal_title：Journal of structural biology

authors： Jeong BC,Park SH,Yoo KS,Shin JS,Song HK

更新日期：2013-07-01 00:00:00

abstract：:Insect flight muscle (IFM) can oscillate at frequencies up to 1000Hz, owing to its capability of stretch activation (SA). It is a highly specialized form of cross striated muscles, and its peculiar features include the IFM-specific isoform of troponin-I (troponin-H or TnH) with an unusually long Pro-Ala-rich extension...

journal_title：Journal of structural biology

authors： Iwamoto H

更新日期：2013-07-01 00:00:00

abstract：:G-protein coupled receptors (GPCRs) are one of the largest families of membrane receptors in eukaryotes. Heterotrimeric G-proteins, composed of α, β and γ subunits, are important molecular switches in the mediation of GPCR signaling. Receptor stimulation after the binding of a suitable ligand leads to G-protein hetero...

journal_title：Journal of structural biology

authors： Baltoumas FA,Theodoropoulou MC,Hamodrakas SJ

更新日期：2013-06-01 00:00:00

abstract：:Upon illumination the visual receptor rhodopsin (Rho) transitions to the activated form Rho(∗), which binds the heterotrimeric G protein, transducin (Gt) causing GDP to GTP exchange and Gt dissociation. Using succinylated concanavalin A (sConA) as a probe, we visualized native Rho dimers solubilized in 1mM n-dodecyl-β...

journal_title：Journal of structural biology

authors： Jastrzebska B,Ringler P,Palczewski K,Engel A

更新日期：2013-05-01 00:00:00

abstract：:Nacre has long served as a model for understanding the biomineralization mechanism and designing bio-inspired materials. However, its basic building blocks, the aragonite tablets, are still under debate in terms of their fine structure at the nanoscale and corresponding formation mechanism. Here, using a field emissio...

journal_title：Journal of structural biology

authors： Zhang G,Xu J

更新日期：2013-04-01 00:00:00

abstract：:Correlative light and electron microscopy is an increasingly popular technique to study complex biological systems at various levels of resolution. Fluorescence microscopy can be employed to scan large areas to localize regions of interest which are then analyzed by electron microscopy to obtain morphological and stru...

journal_title：Journal of structural biology

authors： Faas FG,Bárcena M,Agronskaia AV,Gerritsen HC,Moscicka KB,Diebolder CA,van Driel LF,Limpens RW,Bos E,Ravelli RB,Koning RI,Koster AJ

更新日期：2013-03-01 00:00:00