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At least 235 records · Page 13Linked to original sources
PubMed2004

Local structure in perovskite relaxor ferroelectrics: high-resolution 93Nb 3QMAS NMR.

Solid solutions of (1'-x)Pb(Mg(1/3)Nb(2/3))O3xPb(Sc(1/2)Nb(1/2))O3 (PMN/PSN) have been investigated using high-resolution 93Nb 3-quantum magic-angle spinning nuclear magnetic resonance experiments (3QMAS NMR). In previous MAS NMR investigations, the local B-cation ordering in these relaxor ferroelectric solid solutions was quantitatively determined. However, in conventional one-dimensional MAS spectra the effects of chemical shifts and quadrupole interaction are convoluted; this, in addition to the insufficient resolution, precludes reliable extraction of the values of isotropic chemical shift and quadrupole coupling product. In the current 3QMAS investigation, 93Nb spectra are presented for concentrations x=0, 0.1, 0.2, 0.6, 0.7, and 0.9 at high magnetic field (19.6 T) and fast sample spinning speed (35.7 kHz). Seven narrow peaks and two broad components are observed. The unique high-resolution of the two-dimensional 3QMAS spectra enables unambiguous and consistent assignments of spectral intensities to the specific 28 nearest B-site neighbor (nBn) configurations, (NMg, NSc, NNb) where each number ranges from 0 to 6 and their sum is 6. It is now possible to isolate the isotropic chemical shift and quadrupole coupling product and separately determine their values for most of the 28 nBn configurations. The isotropic chemical shift depends linearly on the number of Mg2+ cations in the configuration; delta iso CS=(13.7 +/- 0.1)NMg-970 +/- 0.4 ppm, regardless of the ratio NSc/NNb. For the seven Nb5+-deficient configurations (NMg, 6-NMg, 0) and the pure niobium configuration (0, 0, 6), the quadrupole coupling products (and hence the electric field gradients) are small (PQ approximately 6-12 MHz) and for the remaining configurations containing small, ferroelectric active Nb5+ ions, the quadrupole coupling products are significantly larger (PQ approximately 40 MHz), indicating larger electric field gradients.

Journal Article↗
PubMed1998

Local structure and dynamics in proteins characterized by hydrogen exchange and mass spectrometry.

Amide hydrogen exchange rates, determined by NMR spectroscopy, have become an important tool that is often used to investigate structure and dynamics of small proteins. Recent developments in mass spectrometry and sample handling methods make possible measurement of deuterium levels at peptide amide linkages in polypeptides. The ability to make these measurements has led to development of the protein fragmentation/mass spectrometry approach for determining amide hydrogen exchange rates in short segments of intact proteins following their incubation in D2O. Partially deuterated proteins are proteolytically fragmented into peptides whose molecular weights are determined by on-line liquid chromatography/mass spectrometry. Deuterium levels, which are determined from the molecular weights of the peptic fragments, can be used to determine amide hydrogen exchange rates. Details of the protein fragmentation/mass spectrometry approach, along with a brief review of the theory of amide hydrogen exchange, are described. The ability to detect and locate minor structural differences in proteins by the protein fragmentation/mass spectrometry approach is illustrated using oxidized and reduced cytochrome c. These results show that oxidation of iron has little effect on the N- and C-terminal regions, but significantly destabilizes the interior regions of cytochrome c. The ability to detect localized unfolding in large proteins is illustrated with aldolase that was equilibrated in acid. Despite the success achieved by NMR spectroscopy for determining amide hydrogen exchange rates, mass spectrometry is advantageous because it permits studies of large proteins, requires only picomoles of protein, and provides a direct measure of structural heterogeneity.

Deuterium↗
PubMed2005

Gene structure, localization and role in oxidative stress of methionine sulfoxide reductase A (MSRA) in the monkey retina.

MSRA (EC 1.8.4.6) is a member of the methionine sulfoxide reductase family that can reduce methionine sulfoxide (MetO) in proteins. This repair function has been shown to protect cells against oxidative damage. In this study we have assembled the complete gene structure of msrA and identified the presence of two distinct putative promoters that generate three different transcripts. These transcripts were cloned by 5'RACE and code for three MSRA isoforms with different N-termini. The different forms of MSRA target to distinct intracellular regions. The main MSRA transcript (msrA1) had been previously shown to target the mitochondria. MsrA2 and 3 originate from a second promoter and target the cytosol and nuclei. In the monkey retina msrA message was detected mainly in the macular RPE-choroid region while its activity was measured mainly in the soluble fractions of fractionated neural retina and RPE-choroid. The MSRA protein is found throughout the retina but is especially abundant at the photoreceptor synapses, ganglion and Müller cells. Interestingly, MSRA was not detected in the mitochondria of the photoreceptor inner segments. The RPE in the peripheral retina shows very low levels of expression but the RPE in the macular region is strongly labeled. Targeted silencing of msrA message rendered cultured RPE cells more sensitive to oxidative damage suggesting a role for MSRA in RPE protection against oxidative stress. Collectively these data suggest MSRA may play an important role in protecting macular RPE from oxidative damage.

Amino Acid Sequence↗
PubMed1986

The effect of HhaI methylation on DNA local structure.

The effect of methylating the central cytosine in the sequence GCGC on the sensitivity to digestion by deoxyribonuclease I was investigated. Examination of five such sites shows that the extra methyl group renders the bond on its 5' side more susceptible to cleavage, and this is interpreted by suggesting that it causes small changes in the local DNA phosphate orientation.

Base Sequence↗
PubMed1996

Local structure analysis of Cu(II)-diazepam complexes by ESR spectroscopy.

CuL(2)X(2) (L = 7-chloro-1,3-dihydro-1-methyl-5-phenyl-3H-1,4-benzodiazepin-2-one, also known as diazepam, X = Cl, Br) complexes have been prepared and investigated by ESR spectroscopy. Powder ESR spectra of these complexes suggest a planar-rhombic distorted local symmetry. The CH(3)Cl solutions spectra show the presence of pseudo-tetrahedral species with a 3d(xy)+4p(z) mixture ground state for the paramagnetic electron. The anisotropic spectra obtained for the Cu(II)-diazepam solution adsorbed on NaY zeolite confirm the existence of a CuN(2)X(2) chromophore.

Journal Article↗
PubMed2001

Geometric local structure at the Mn site in charge-ordered mixed valence manganites.

An extensive study of Mn K-edge absorption sepctroscopy has been carried out in La(1-x)Ca(x)MnO3 and Tb(1-x)Ca(x)MnO3 (x=0, 0.33, 0.5, 0.67, 1) series as a function of temperature. The EXAFS analysis for the charge ordering compounds (x > or = 0.5) shows the presence of a static distortion of the MnO6 octahedron in the whole temperature range. However, this local distortion is lower than the distortion found for Jahn-Teller compounds. Magnetoresistive compounds (x=0.33) show a regular octahedron in the low temperature metallic phase. Instead, no changes are found for the first coordination shell (Mn-O) across the charge ordering transition while Mn-Mn distribution shows minor variations with the temperature. The structural analysis of the second coordination shell suggests that the Mn-O-Mn angle is the most relevant parameter to describe the electric and magnetic behaviour of these compounds.

Journal Article↗
PubMed2003

Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2.

Several autoinflammatory diseases with distinct clinical manifestations have been associated with sequence variations in the gene products PYPAF1/CIAS1 and NOD2/CARD15. Both proteins belong to the PYD/CARD-containing family of apoptosis regulators and activators of pro-inflammatory caspases. To gain insight into the dysfunctional role of sequence alterations, we assembled a structure-based multiple sequence alignment of family members and related proteins. This allowed us to analyze the putative effect of the alterations on the function of nucleotide-binding (NACHT) and leucine-rich repeat (LRR) domains shared by the family members. In support of this analysis, we carefully selected template structures for the NACHT and LRR domains and mapped the genetic variations onto 3D domain models. Additionally, we propose a model of the NACHT and LRR domain complex. Our study revealed that many of the disease-associated sequence variants are located close to highly conserved sequence regions of functional relevance and are spatially adjacent in the predicted 3D structure. The implications on the domain functions such as NTP-hydrolysis or oligomerization are discussed.

Amino Acid Sequence↗
PubMed2005

Spatially resolved imaging of inhomogeneous charge transfer behavior in polymorphous molybdenum oxide. I. Correlation of localized structural, electronic, and chemical properties using conductive probe atomic force microscopy and Raman microprobe spectroscopy.

A detailed study of electrochemically deposited molybdenum oxide thin films has been carried out after they were sintered at 250 degrees C. Conductive probe atomic force microscopy (CP-AFM), Raman microscopy, and X-ray photoelectron spectroscopy (XPS) techniques were employed to assess the complex structural, electronic, and compositional properties of these films. Spatially resolved Raman microprobe spectroscopy studies reveal that sintered molybdenum oxide is polymorphous and phase segregated with three types of domains observed comprising orthorhombic alpha-MoO3, monoclinic beta-MoO3, and intermixed alpha-/beta-MoO3. CP-AFM studies conducted in concert with Raman microprobe spectroscopy allowed for correlation between specific compositional regions and localized electronic properties. Single point tunneling spectroscopy studies of chemically distinct regions show semiconducting current-voltage (I-V) behavior with the beta-MoO3 polymorph exhibiting higher electronic conductivity than intermixed alpha-/beta-MoO3 or microcrystalline alpha-MoO3 domains. XPS valence level spectra of beta-MoO3 films display a small structured band near the Fermi level, indicative of an increased concentration of oxygen vacancies. This accounts for the greatly enhanced electronic conductivity of beta-MoO3 as these positively charged cationic defects (anion vacancies) act to trap excess electrons. Connections between structural features, electronic properties, and chemical composition are established and discussed. Importantly, this work highlights the value of using spatially resolved techniques for correlating structural and compositional features with electrochemical behaviors of disordered, mixed-phase lithium insertion oxides.

Journal Article↗
PubMed1975

The ultra-structural localization of enzyme activity in unfixed sections.

A technique is described for using conventional unfixed cryostat sections for localising enzyme activities in the electron microscope. The sections are incubated on the slide in the presence of a stabiliser, and then only fixed and embedded after the reaction is complete. Thin sections can then be cut of the reacted section, for electron microscopy. The present article shows that good ultra-structural morphology is retained during the freezing and cutting stages, and although some loss of detail occurs after the incubation, sub-cellular membranes are still intact, and membrane-associated reaction product can be clearly seen.

Animals↗
PubMed2000

Local Structure Evolution in Particle Network Formation Studied by Brownian Dynamics Simulation.

The effect of solid content and colloidal interactions on the structure of forming networks of colloidal particles is studied by Brownian dynamics simulation. The different situations are compared in terms of the pair distribution function and the distribution of nearest neighbors around each particle. The results indicate that, in fast coagulation, the higher solid contents lead to a freezing-in of the liquid structure. Nevertheless, this effect can be reduced substantially by the introduction of a shallow secondary minimum and an energy barrier in the interaction potential. However, the structures resulting from such slow coagulation show a substantial degree of porosity, larger than those produced at the same solid content but by fast coagulation. It is also shown how the porosity (defined on a few particle diameters) is reflected in the distribution of nearest neighbors around the center particle, i.e., the very local conformation in the particle network. Fractal analysis shows that, at the relatively high volume fractions considered in this study, no intermediate fractal regime exists. Copyright 2000 Academic Press.

Journal Article↗
PubMed1983

Structural localization of the elements of the acetylcholine system in the rat cerebellum.

The elements of the acetylcholine system (choline acetyltransferase, acetylcholinesterase, acetylcholine receptors) were analysed in the cerebellum of the rat by histochemical and biochemical means. All the elements were found. Besides the granular layer, the molecular layer exerts CAT activity. The 3H-QNB binding site is highest in the molecular layer and lowest in the intracerebellar nuclei, while the 125I-alpha-bungarotoxin distribution in these structures is the opposite. The results support the view that cholinergic transmission may be present in the rat cerebellum.

Acetylcholine↗
PubMed2003

Discovering local structure in gene expression data: the order-preserving submatrix problem.

This paper concerns the discovery of patterns in gene expression matrices, in which each element gives the expression level of a given gene in a given experiment. Most existing methods for pattern discovery in such matrices are based on clustering genes by comparing their expression levels in all experiments, or clustering experiments by comparing their expression levels for all genes. Our work goes beyond such global approaches by looking for local patterns that manifest themselves when we focus simultaneously on a subset G of the genes and a subset T of the experiments. Specifically, we look for order-preserving submatrices (OPSMs), in which the expression levels of all genes induce the same linear ordering of the experiments (we show that the OPSM search problem is NP-hard in the worst case). Such a pattern might arise, for example, if the experiments in T represent distinct stages in the progress of a disease or in a cellular process and the expression levels of all genes in G vary across the stages in the same way. We define a probabilistic model in which an OPSM is hidden within an otherwise random matrix. Guided by this model, we develop an efficient algorithm for finding the hidden OPSM in the random matrix. In data generated according to the model, the algorithm recovers the hidden OPSM with a very high success rate. Application of the methods to breast cancer data seem to reveal significant local patterns.

Algorithms↗
PubMed1986

Hydrophobic interactions in the major groove can influence DNA local structure.

We have considered hydrophobic interactions among aliphatic hydrocarbon groups in A/T sequences. The slightly overwound sequences (T)n.(A)n yield structures with tightly stacked methyl groups along one side of the major groove. The sequence TTAA may yield a sharp bend by folding together the two pairs of stacked methyls on the opposite sides of the major groove. Thus the sequence can affect the formation of either a smooth bend or a sharp kink. These sequence dependent local conformations may be related to a number of biological results.

Base Composition↗
PubMed1978

Studies on the mode of action of phenylmercuric borate on Escherichia coli. I. Structural localization and kinetics of incorporation.

Phenylmercuric borate (PHB) is very rapidly incorporated into the cells of Escherichia coli, and binds directly to its sites of fixation. The rapid incorporation of PHB probably results from the lipophilic character of the [phenylmercuric]+ cation. The distribution of PHB in the cell is fairly uniform if one compares with that of the proteins. This shows the low specificity of PHB with regard to proteins, all of which appear to be potential sites for fixation. However, from the structural point of view, PHB is more differentiated in its distribution. The cell wall of E. coli and the soluble cytoplasmic fraction do not constitute important sites of fixation. On the contrary, the cytoplasmic membrane appears to be a preferential site of fixation. Moreover, it is very probable that the distribution of PHB in vivo should be even more likely at the cytoplasmic membrane since the process of homogenization of the cells solubilizes a large part of the proteins associated to the membrane. On the membrane, an important part of PHB seems to be associated with the ribosomes and particularly to the ribosomal proteins.

Bacterial Proteins↗
PubMed1962

The fine structural localization of acetylcholinesterase at the myoneural junction.

A study of the cytochemical localization of acetylcholiriesterase activity, combining histochemistry with electron microscopy, showed that the final product of the reaction, which was deposited at or near enzyme sites, occurred at four places in the myoneural junction. These included: plasma membrane of the muscle covering the junctional folds, the primary and secondary synaptic clefts, parts of the plasma membrane covering the axon terminal, and vesicular structures in the terminal axoplasm. No reaction occurred in the presence of 10(-4) eserine or DFP, whereas 10(-5) DFP inhibited the reaction at all sites except in the vesicles of the terminal axon. These findings are discussed with reference to the histochemical method used and to the occurrence of esterolytic activity in the vesicles, as well as to some of the current hypotheses concerning the relationship of the site of acetylcholinesterase and synaptic transmission.

Acetylcholinesterase↗
PubMed1999

Maroteaux-lamy syndrome: five novel mutations and their structural localization.

Maroteaux-Lamy syndrome (mucopolysaccharidosis type VI, MPS VI) is an autosomal recessive disorder due to the deficiency of the lysosomal enzyme N-acetylgalactosamine-4-sulfatase (arylsulfatase B, ASB). Mutation analysis in Maroteaux-Lamy syndrome resulted in the identification of approximately 40 molecular defects underlying a great genetic heterogeneity. Here we report five novel mutations in Italian subjects: S65F, P116H, R315Q, Q503X, P531R; each defect was confirmed by restriction enzyme or amplification refractory mutation system (ARMS) analysis. We also performed a three-dimensional (3-D) structure analysis of the alterations identified by us, and of an additional 22 point mutations reported by other groups, in an attempt to draw helpful information about their possible effects on protein conformation.

Binding Sites↗
PubMed1980

Fine structural localization of calcium binding sites in the neuromuscular junction.

By means of electron cytochemical analysis of rat neuromuscular junctions subjected to perfusion with a calcium-containing (5 mM) aldehyde fixative, two kinds of presynaptic calcium binding sites were demonstrated. "A" sites are located above openings of junctional folds; these triangular elements are identical with presynaptic protrusions of the active zone and probably comprise calcium channels of the presynaptic membrane, "B" sites, located within the terminal axoplasm, are associated to multivesicular bodies probably accumulating surplus intracellular calcium. This fine structural arrangement enables a highly parsimonious usage of extracellular calcium in inducing release of acetylcholine from synaptic vesicles. Junctional folds of the postsynaptic membrane may funnel calcium ions exactly to spatially restricted calcium channels. Having entered the terminal through the channels opened by the arrival of nerve action potential, calcium ions may exert their action upon synaptic vesicles accumulated in the closest vicinity by means of stripping off hydration barriers and by inducing membrane fusions, that finally result in quantal release of acetylcholine from the terminal.

Animals↗
PubMed1979

Fine structural localization of alkaline phosphatase in rat ovum during cleavage.

On a submicroscopic level alkaline phosphatase activity was demonstrated by cytochemical methods in all stages of segmenting rat ova under survey, i.e. in the unfertilized and fertilized ovum, in the two-, four- and eight-cell stages and in the blastocyst. The reaction product was present in some cytoplasmic organelles as well as on cell membranes. A considerable number of cytoplasmic organelles with alkaline phosphatase activity was found in all stages from the one-cell up to the eight-cell stage. The reaction product was deposited in the tubules and vesicles of the smooth endoplasmic reticulum, in the nuclear envelope and in the Golgi complex as well. Some multivesicular bodies, autophagic vacuoles and majority of residual bodies out of the secondary lysosomes showed enzymatic activity. In the multicellular stages no significant differences were observed between the individual blastomeres in the incidence and distribution of the alkaline phosphatase activity. On the blastocyst-stage was found a low incidence of enzymatically active cytoplasmic organelles. Alkaline phosphatase activity was demonstrated in some minute vesicles below the cell membrane and in some secondary lysosomes. No essential differences were found between the cells of the embryoblast and the cells of the trophoblast in the incidence of enzymatically active structures. In the one-cell stage the activity of alkaline phosphatase was present on the cell membrane only sporadically, in the two- and four-cell stages enzymatic activity was found in this localization in a third of all specimen. In the eight-cell stage alkaline phosphatase activity was demonstrated on the cell membranes of all blastomeres. In the blastocyst the reaction product was deposited regularly on the membranes of the trophoblastic cells turned towards the zone pellucida, frequently on membranes of mutual tactile cells of the trophoblast and the embryoblast and only sporadically on cell membranes limiting the blastocyst cavity.

Alkaline Phosphatase↗