Abstract：
:Regulation of gene transcription in both prokaryotes and eukaryotes involves the formation of DNA-multiprotein complexes. These complexes build a precise three-dimensional topology allowing communication between distal regions of DNA. The switch from early to late transcription in bacteriophage Ø29 involves binding of viral proteins, p4 and p6, to a region of the genome containing the early promoters A2c and A2b and the late promoter A3. Atomic force microscopy imaging under aqueous buffering conditions of complexes built after DNA incubation with proteins p4 and p6 shows the formation of a nucleoprotein arrangement with consistent morphology. These two low specificity DNA binding proteins are capable of bending 160 base pairs into a nucleoprotein-hairpin stable enough to be imaged by AFM. The functional implications of this nucleoprotein-hairpin in the coordinated regulation of early and late promoters are discussed.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
del Arroyo PG,Vélez M,Piétrement O,Salas M,Carrascosa JL,Camacho Adoi
10.1016/j.jsb.2009.06.016subject
Has Abstractpub_date
2009-12-01 00:00:00pages
444-51issue
3eissn
1047-8477issn
1095-8657pii
S1047-8477(09)00167-1journal_volume
168pub_type
杂志文章abstract：:Lipocalin-type prostaglandin D synthase (L-PGDS) acts as both a PGD(2) synthase and an extracellular transporter for small lipophilic molecules. From a series of biochemical studies, it has been found that L-PGDS has an ability to bind a variety of lipophilic ligands such as biliverdin, bilirubin and retinoids in vitr...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.10.005
更新日期：2010-02-01 00:00:00
abstract：:Traditional single particle reconstruction methods use either the Fourier or the delta function basis to represent the particle density map. This paper proposes a more flexible algorithm that adaptively chooses the basis based on the data. Because the basis adapts to the data, the reconstruction resolution and signal-...
journal_title：Journal of structural biology
pub_type： 杂志文章
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abstract：:Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2001.4443
更新日期：2001-12-01 00:00:00
abstract：:In situ hybridization (ISH) is a widely applied technique used for visualizing specific nucleic acid sequences at chromosomal, cytologic, and histologic levels. It sometimes fails, however, to demonstrate precise cell identity, early stages of gene expression and variants of alternative splicing because of its limited...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.09.010
更新日期：2006-01-01 00:00:00
abstract：:Formation of filaments by the Ure2 protein constitutes the molecular mechanism of the [URE3] prion in yeast. According to the "amyloid backbone" model, the N-terminal asparagine-rich domains of Ure2p polymerize to form an amyloid core fibril that is surrounded by C-terminal domains in their native conformation. Protea...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.02.007
更新日期：2005-05-01 00:00:00
abstract：:A structural analysis of cells that contained the interferon-alpha-induced lupus inclusions (LI) was performed using a high-voltage electron microscope to determine the exact cellular location of LI and their association with normal cell organelles. LI were induced in the human B lymphoblastoid cell line, Daudi, by cu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(92)90004-t
更新日期：1992-01-01 00:00:00
abstract：:In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs fr...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.03.006
更新日期：2017-05-01 00:00:00
abstract：:REMORINs are nanodomain-organized proteins located in the plasma membrane and involved in cellular responses in plants. The dynamic assembly of the membrane nanodomains represents an essential tool of the versatile membrane barriers to control and modulate cellular functions. Nevertheless, the assembly mechanisms and ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.02.003
更新日期：2019-04-01 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
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.04.006
更新日期：2014-07-01 00:00:00
abstract：:We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchm...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.10.011
更新日期：2012-02-01 00:00:00
abstract：:Protein tertiary structure modeling is a critical step for the interpretation of three dimensional (3D) election microscopy density. Our group participated the 2015/2016 EM Model Challenge using the MAINMAST software for a de novo main chain modeling. The software generates local dense points using the mean shifting a...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.07.013
更新日期：2018-11-01 00:00:00
abstract：:The 32 kDa hydrophilic and acidic enamelin, the most stable cleavage fragment of the enamel specific glycoprotein, is believed to play vital roles in controlling crystal nucleation or growth during enamel biomineralization. Circular dichroism and Fourier transform infrared spectra demonstrate that the secondary struct...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.04.007
更新日期：2008-07-01 00:00:00
abstract：:The graphics processing unit (GPU), which originally was used exclusively for visualization purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through the development of elaborate interfaces, the GPU can be used to process data and deal with computationally intensive applications. The spe...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.07.006
更新日期：2008-10-01 00:00:00
abstract：:Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large nu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2001.4415
更新日期：2001-09-01 00:00:00
abstract：:Charge contrast imaging (CCI) is a dynamic phenomenon recently reported in insulating and semiconducting materials imaged with low vacuum or variable pressure scanning electron microscopes (SEM). Data presented in this paper illustrates that CCI can also be applied to biominerals and biological soft-tissues and that u...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.04.004
更新日期：2006-09-01 00:00:00
abstract：:The phycobilisome photosynthetic antenna complex, found in cyanobacteria and red-algae, interacts with proteins expressed specifically to deal with different forms of physiological stress. Under conditions of nutrient starvation, the NblA protein is required for the process that leads to phycobilisome degradation and ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.10.021
更新日期：2007-04-01 00:00:00
abstract：:The β-carbonic anhydrases (β-CAs) are widely distributed zinc-metalloenzymes that play essential roles in growth, survival, development and virulence in fungi. The majority of filamentous ascomycetes possess multiple β-CA isoforms among which major and minor forms have been characterized. We examined the catalytic beh...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.07.011
更新日期：2019-10-01 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
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.12.004
更新日期：2013-03-01 00:00:00
abstract：:The morphologic effects of different sulfur-substituted mono- and dicarboxylic fatty acids on rat hepatocytes have been examined. The substance 1,10-biscarboxymethylthiodecane (BCMTD) is blocked for both beta- and omega-oxidation, whereas 1-monocarboxymethylthiodecane (CMTTD) is only non-beta-oxidizable. At equimolar ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(90)90044-d
更新日期：1990-05-01 00:00:00
abstract：:Molecular genetic studies with prokaryotic microorganisms reveal that many different molecular processes contribute to the formation of spontaneous mutations. Besides infidelities in DNA replication and the consequences of environmental mutagens, enzyme-mediated DNA rearrangements bring about important, evolutionarily...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/1047-8477(90)90064-j
更新日期：1990-07-01 00:00:00
abstract：:Structures of highly ordered biological bundles have unique features which call for special experimental and computational methods in electron cryomicroscopy. They can be considered as three-dimensional quasi-crystals and reconstructed using a crystallographic approach. However, they are neither "infinitely" large wit...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3916
更新日期：1997-12-01 00:00:00
abstract：:In the cornea, the precise organisation of fibrillar collagen and associated proteoglycans comprising the stromal extracellular matrix plays a major role in governing tissue form and function. Recently, abnormal collagen alignment was noted in the misshapen corneas of mature chickens affected by the retinopathy, globe...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.01.009
更新日期：2009-05-01 00:00:00
abstract：:A simple, fast and efficient noise-reduction protocol for three-dimensional electron tomographic reconstructions of biological material is presented. The approach is based on iterative application of median filtering and shows promise for automatic noise reduction as a pre-processor for automated data analysis tools w...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.10.030
更新日期：2007-05-01 00:00:00
abstract：:Raman spectroscopy was used to determine the mineralogical composition of the calcareous tubes of three species belonging to the family Cirratulidae. In all three cases, the tubes were found to be aragonitic, confirming previous inferences based on EDX and thin section studies, and corroborated by new EDX analyses rev...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.05.010
更新日期：2010-09-01 00:00:00
abstract：:We analyzed a tertiary structure of systemin, the first identified polypeptide plant hormone, using two-dimensional NMR spectroscopy. From these data and molecular dynamics calculations we concluded that the peptide can adopt a Z-like-beta-sheet structure, which has previously been found in many specific DNA-binding p...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1995.1026
更新日期：1995-07-01 00:00:00
abstract：:The epithelial cell lining of the respiratory groove of Alma emini, an oligochaete glossoscolecid worm that lives in a hydrogen sulfide (H2S)-rich tropical swamp, was investigated by transmission electron microscopy to determine the underlying structural adaptations which enable the worm to subsist in a highly inimica...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4000
更新日期：1998-01-01 00:00:00
abstract：:Microbial type III polyketide synthases (PKSs) have revealed remarkable mechanistic as well as functional versatility. Recently, a type III PKS homolog from Azotobacter has been implicated in the biosynthesis of resorcinolic lipids, thus adding a new functional significance to this class of proteins. Here, we report t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.02.009
更新日期：2008-06-01 00:00:00
abstract：:The massive basal skeleton of a few remnant living hypercalcified sponges rediscovered since the 1960s are valuable representatives of ancient calcium carbonate biomineralization mechanisms in basal Metazoa. A multi-scale mineralogical characterization of the easily accessible Mediterranean living hypercalcified spong...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.08.008
更新日期：2011-12-01 00:00:00
abstract：:Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum (opium poppy), which belongs to the non-heme 2-oxoglutarate/Fe(II)-dependent dioxygenases (ODD) family, is a key enzyme in the morphine biosynthesis pathway. Initially, T6ODM was characterized as an enzyme catalyzing O-demethylation of thebaine to neopinone and ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2018.01.007
更新日期：2018-06-01 00:00:00
abstract：:Immunoelectron microscopy of serial sections of leaf cells of wheat doubly infected by wheat streak mosaic virus and Agropyron mosaic virus or wheat spindle streak mosaic virus showed that structural proteins or virions associated only with homologous cylindrical inclusions (CI) or with self in aggregates. CI protein ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1993.1021
更新日期：1993-05-01 00:00:00
