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PubMed1967

Fine structural localization of a blood-brain barrier to exogenous peroxidase.

Horseradish peroxidase was administered to mice by intravenous injection, and its distribution in cerebral cortex studied with a recently available technique for localizing peroxidase with the electron microscope. Brains were fixed by either immersion or vascular perfusion 10-60 min after administration of various doses of peroxidase. Exogenous peroxidase was localized in the lumina of blood vessels and in some micropinocytotic vesicles within endothelial cells; none was found beyond the vascular endothelium. Micropinocytotic vesicles were few in number and did not appear to transport peroxidase while tight junctions between endothelial cells were probably responsible for preventing its intercellular passage. Our findings therefore localize, at a fine structural level, a "barrier" to the passage of peroxidase at the endothelium of vessels in the cerebral cortex. The significance of these findings is discussed, particularly with reference to a recent study in which similar techniques were applied to capillaries in heart and skeletal muscle.

Animals↗

PubMed2004

Structure of circularly permuted DsbA(Q100T99): preserved global fold and local structural adjustments.

The thiol-disulfide oxidoreductase DsbA is required for efficient formation of disulfide bonds in the Escherichia coli periplasm. The enzyme is the strongest oxidant of the family of thioredoxin-like proteins and three-dimensional structures of both oxidized and reduced forms are known. DsbA consists of a catalytic thioredoxin-like domain and a helical domain that is inserted into the thioredoxin motif. Here, the X-ray structure of a circularly permuted variant, cpDsbA(Q100T99), is reported in which the natural termini are joined by the pentapeptide linker GGGTG, leading to a continuous thioredoxin domain, and new termini that have been introduced in the helical domain by breaking the peptide bond Thr99-Gln100. cpDsbA(Q100T99) is catalytically active in vivo and in vitro. The crystal structure of oxidized cpDsbA(Q100T99), determined by molecular replacement at 2.4 A resolution, was found to be very similar to that of wild-type DsbA. The lower thermodynamic stability of cpDsbA(Q100T99) relative to DsbA is associated with small structural changes within the molecule, especially near the new termini and the circularizing linker. The active-site helices and adjacent loops display increased flexibility compared with oxidized DsbA.

Amino Acid Motifs↗

PubMed2006

Probing the local structure of liquid water by X-ray absorption spectroscopy.

It was recently suggested that liquid water primarily comprises hydrogen-bonded rings and chains, as opposed to the traditionally accepted locally tetrahedral structure (Wernet et al. Science 2004, 304, 995). This controversial conclusion was primarily based on comparison between experimental and calculated X-ray absorption spectra (XAS) using computer-generated ice-like 11-molecule clusters. Here we present calculations which conclusively show that when hydrogen-bonding configurations are chosen randomly, the calculated XAS does not reproduce the experimental XAS regardless of the bonding model employed (i.e., rings and chains vs tetrahedral). Furthermore, we also present an analysis of a recently introduced asymmetric water potential (Soper, A. K. J. Phys.: Condens. Matter 2005, 17, S3273), which is representative of the rings and chains structure, and make comparisons with the standard SPC/E potential, which represents the locally tetrahedral structure. We find that the calculated XAS from both potentials is inconsistent with the experimental XAS. However, we also show the calculated electric field distribution from the rings and chains structure is strongly bimodal and highly inconsistent with the experimental Raman spectrum, thus casting serious doubt on the validity of the rings and chains model for liquid water.

Journal Article↗

PubMed2000

Stationary and drifting localized structures near a multiple bifurcation point

Localized states embedded in a patterned background are found in numerical simulations of spontaneous pattern formation in a spin-1/2 atomic system with optical feedback. In the vicinity of a parameter region with bistability between two homogeneous states large amplitude peaks as well as dark holes exist as stable localized states on a hexagonal background. Moreover, resonant interaction between oscillatory and stationary inhomogeneous modes produces a nonstationary background which may force the localized states to drift.

Journal Article↗

PubMed2001

pH-dependent local structure of ferricytochrome c studied by x-ray absorption spectroscopy.

We have studied, using x-ray absorption spectroscopy by synchrotron radiation, the native state of the horse heart cytochrome c (N), the HCl denatured state (U(1) at pH 2), the NaOH denatured state (U(2) at pH 12), the intermediate HCl induced state (A(1) at pH 0.5), and the intermediate NaCl induced state (A(2) at pH 2). Although many results concerning the native and denatured states of this protein have been published, a site-specific structure analysis of the denatured and intermediate solvent induced states has never been attempted before. Model systems and myoglobin in different states of coordination are compared with cytochrome c spectra to have insight into the protein site structure in our experimental conditions. New features are evidenced by our results: 1) x-ray absorption near edge structure (XANES) of the HCl intermediate state (A(1)) presents typical structures of a pentacoordinate Fe(III) system, and 2) local site structures of the two intermediate states (A(1) and A(2)) are different.

Absorptiometry, Photon↗

PubMed1991

Local structures in unfolded lysozyme and correlation with secondary structures in the native conformation: helix-forming or -breaking propensity of peptide segments.

CD spectra of reduced and S-3-(trimethylated amino) propylated lysozyme (TMAP lysozyme) have been measured in various solutions containing guanidine hydrochloride or trifluoroethanol (TFE). The CD spectra indicate that there remain residual secondary structures in protein in aqueous solution. The addition of TFE further promotes the formation of secondary structures. In order to examine whether secondary structures are evenly induced over all the polypeptide chain, or locally at particular segments, the limited proteolysis of TMAP lysozyme by trypsin has been performed, and the CD spectra of all the final and intermediate products have been observed in solutions containing TFE. As a result, the fragments vary in a helix-forming propensity. The CD spectra of peptide fragments T5, T7, T9T10, T12T13, T14T15T16, and T17T18 are not significantly affected by the addition of TFE, where T refers to the nomenclature of R.E. Canfield [(1963), Journal of Biological Chemistry, Vol. 238, pp. 2691-2697]. They are fragments of a helix-breaking propensity. On the other hand, fragment I2 composed of T1-T4, and fragments T6T7, T8, and T11, attain secondary structures with the addition of TFE. They are fragments of a helix-forming propensity. Further, it is found that the fragments of a helix-forming propensity just correspond to the helical segments in native lysozyme. We examine the interactions between neighboring fragments, which contribute to the stabilization of local structures along the polypeptide chain.

Amino Acids↗

PubMedDate not supplied

Brain structure localization in positron emission tomography: comparison of magnetic resonance imaging and a stereotactic method.

A method commonly used for localization of brain regions on positron emission tomographic (PET) images is direct visualization and designation of structure on the image itself. This technique, however, is limited to portions of the brain having sufficient differential radionuclide uptake to permit the recognition of structure by observers familiar with brain anatomy. Two other methods commonly used instead of direct visualization are magnetic resonance imaging (MRI) and stereotactic methods of localization. This report compares the accuracy of a MRI method versus a stereotactic method of brain structure localization of PET. The three localization methods were analyzed for sixteen different brain regions in 5 different subjects by two independent observers. The results were converted to PET pixel size (1 pixel = .127 cm) for comparison. MRI localization differed from direct visualization by a mean and standard deviation of approximately 2 +/- 1 pixels in both the X and Y dimensions. Stereotactic localization differed from direct visualization by approximately 2 +/- 1 pixels in the X dimension and by approximately 6 +/- 2 pixels in the Y dimension. This larger variation seen with the stereotactic method may be attributed to the questionable assumption of linearity of structure location with respect to size of the inner table of the calvarium.

Adult↗

PubMed1994

Solution structure of a peptide fragment of human alpha-lactalbumin in trifluoroethanol: a model for local structure in the molten globule.

BACKGROUND: At low pH, human alpha-lactalbumin forms a partly folded molten globule state that contains a non-native clustering of the side chains of Tyr103, Trp104 and His107. In order to understand the conformation of this region of the protein in the molten globule state, we investigated the structure of a peptide corresponding to residues 101-110 of human alpha-lactalbumin in trifluoroethanol. RESULTS: We determined the structure of the 101-110 peptide from an NMR data set of 145 nuclear Overhauser effects and nine 3JHN alpha coupling constants, using an ensemble calculation approach to take into account the possibilities of conformational averaging of the data. The backbone of residues 3-10 in the peptide adopts a series of turns, that involving residues 5-8 being the best defined, while the side chains of residues 1, 3, 4, 5, 6 and 7 form a hydrophobic cluster. CONCLUSIONS: The peptide conformation differs from that previously determined for residues 101-110 in crystal structures of native alpha-lactalbumin determined at both high and low pH, particularly in the relative orientations of the side chains. The series of turns seen in the peptide could, however, be related to the alpha-helical structure seen for residues 104-111 in crystals at high pH, and may be important in the molten globule state for bringing the peptide chain into a compact conformation where favourable interactions between the side chains can occur.

Amino Acid Sequence↗

PubMed1978

Characterisation of a local structure in the synthetic parathyroid hormone fragment 1--34 by 1H nuclear-magnetic-resonance techniques.

Previous studies had shown that the molecular conformation of the synthetic human parathyroid hormone fragment 1--34 in dilute aqueous solution contained a local non-random structure formed by the four consecutive residues--Val-21--GIn-22--Trp-23--Leu-24--. This paper gives a detailed description of this local spatial structure obtained from high resolution 1H NMR studies at 360 MHZ of several peptide analogs of the partial sequence 20--24. The most important spectral parameters were high-field shifts of the alpha and gamma protons of Val-21, the spin-spin coupling constants related to the rotamer populations of the side-chains of Val-21 and Trp-23, and pH titration shifts of the amide proton resonances. It was found that the backbone fragment 20--24 is so arranged that the side-chain of Val-21 is located next to the indole ring plane of Trp-23; evidence is presented that this non-random structure is mainly stabilized by hydrophobic interactions between the side-chains of Val-21 and Trp-23. The thermal population of the observed molecular structure at room temperature was estimated from the nuclear magnetic resonance data to be approximately 20%.

Amino Acid Sequence↗

PubMed2005

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%.

MOTIVATION: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in sequence. Even though the number of available methods is growing, it is still of interest to pairwise detect two genes with low sequence similarity, where the genes are part of a larger genomic region. RESULTS: Here we present such an approach for pairwise local alignment which is based on foldalign and the Sankoff algorithm for simultaneous structural alignment of multiple sequences. We include the ability to conduct mutual scans of two sequences of arbitrary length while searching for common local structural motifs of some maximum length. This drastically reduces the complexity of the algorithm. The scoring scheme includes structural parameters corresponding to those available for free energy as well as for substitution matrices similar to RIBOSUM. The new foldalign implementation is tested on a dataset where the ncRNAs and eleRNAs have sequence similarity <40% and where the ncRNAs and eleRNAs are energetically indistinguishable from the surrounding genomic sequence context. The method is tested in two ways: (1) its ability to find the common structure between the genes only and (2) its ability to locate ncRNAs and eleRNAs in a genomic context. In case (1), it makes sense to compare with methods like Dynalign, and the performances are very similar, but foldalign is substantially faster. The structure prediction performance for a family is typically around 0.7 using Matthews correlation coefficient. In case (2), the algorithm is successful at locating RNA families with an average sensitivity of 0.8 and a positive predictive value of 0.9 using a BLAST-like hit selection scheme. AVAILABILITY: The program is available online at http://foldalign.kvl.dk/

Algorithms↗

PubMed2004

Cavity light bullets: three-dimensional localized structures in a nonlinear optical resonator.

We consider the paraxial model for a nonlinear resonator with a saturable absorber beyond the mean-field limit. For accessible parametric domains we observe total radiation confinement and the formation of 3D localized bright structures. Different from freely propagating light bullets, here the self-organization proceeds from the resonator feedback, combined with diffraction and nonlinearity. Such "cavity" light bullets can be independently excited and erased by appropriate pulses, and once created, they endlessly travel the cavity round-trip.

Journal Article↗

PubMed1994

Selective attention to global and local structure of objects: alternative measures of nontarget processing.

When individuals are asked to report either the global or the local level of structure in a stimulus pattern located inside a relevant object, distractors located within an irrelevant object will interfere only if they are at the same level of structure as that of the target item (Briand, 1993; Paquet & Merikle, 1988). The basis of this level-specific filtering is unclear, as is the true level of semantic analysis for the ignored items. In the present series of experiments, multiple measures of nontarget processing were used to assess concurrent interference, negative priming, and a category effect supposedly reflecting a more abstract level of semantic analysis. These different indicants were assessed in three experiments in which form, color, or a spatial precue was used to direct attention to the relevant stimulus pattern. Overall, cuing by form produced poorer spatial selectivity, whereas spatial precues and color led to better selectivity. However, the three measures of nontarget processing were not equally affected by these manipulations, with global information showing more evidence for semantic analysis than for local analysis regardless of the type of selection cue used. The results suggest that inhibition is not the basis of target selection when ignored items are local, but that it may be used when global items are ignored.

Adult↗

PubMed2006

Molecular dynamics study of polarizability anisotropy relaxation in aromatic liquids and its connection with local structure.

The collective polarizability anisotropy dynamics in a set of three aromatic liquids, benzene (Bz), hexafluorobenzene (HFB), and 1,3,5-trifluorobenzene (TFB), has been studied by molecular dynamics simulation. These liquids have very similar shapes, but different electrostatic interactions due to opposite polarities of C-H and C-F bonds, giving rise to different local intermolecular structures in the liquid phase. We have investigated how these structural arrangements affect polarizability anisotropy dynamics observed in optical Kerr-effect (OKE) spectroscopy. We have modeled the interaction-induced polarizability with the first-order dipole-induced dipole approximation, with the molecular polarizability distributed over the carbon sites. Local contributions to the librational OKE spectrum were computed separately for molecules participating in parallel or perpendicular relative orientations within the first coordination shell. We found that the relative locations of parallel and perpendicular librational bands of the OKE spectra are closely related to the corresponding pair energy distributions of the closest four neighbors of a given molecule, corresponding to a model of a harmonic oscillator in a cage of nearest neighbors. This model predicts higher librational frequencies for more attractive intermolecular interactions, which in all three liquids correspond to parallel local arrangements. On the diffusive orientational time scale, all three liquids exhibit slower relaxation of molecules in parallel arrangements, although the difference in relaxation rates is substantial only in TFB, which has the strongest tendency toward parallel stacking. The analysis of the collective polarizability relaxation was performed using two different approaches, the projection scheme (J. Chem. Phys. 1980, 72, 2801) and the theory developed by Steele (Mol. Phys. 1987, 61, 1031) for the second time derivatives applied to collective time correlations. Both approaches allow the decomposition of the OKE response into contributions from orientational relaxation and other dynamical processes. We find that they lead to different predictions on how the response depends on collective reorientation and processes arising from fluctuations in the interaction-induced polarizability. We discuss the reasons for these differences and the advantages and disadvantages of the two analysis schemes.

Journal Article↗

PubMed1980

Structural localization of calcium binding sites in the neuromuscular junction after supramaximal stimulation.

Rat motor end plates were supramaxillary stimulated by means of acute systemic inhibition of acetylcholinesterase. Electron micrographs obtained from samples subjected to perfusion with a calcium-containing (5 mM) aldehyde fixative demonstrates profound alterations in the fine structures and localization of calcium binding sites, markedly differring from those prevailing in the resting state and/or under conditions of physiological function. Neither "A" sites at the active zones of the synapse, nor "B" sites within the terminal proper, which are apparent in the resting state, do bind calcium after supramaximal stimulation which is characterized by a conspicuous vacuolization of the sole plate, brought about by destruction of the post-synaptic mitochondria. Calcium binding after supramaximal stimulation is partly postsynaptic (in granules of varying sizes within the sole plate) partly presynaptic (in synaptic vesicles, as well as in the whole extent of the presynaptic membrane). Limited resolving power of light microscopy and artificial translocation of the reaction product of the histochemical reaction may account for the earlier interpretation of exclusively post-synaptic localization of calcium after supramaximal stimulation.

Acetylcholinesterase↗

PubMed2004

The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region.

The gene-silencing effect of short interfering RNA (siRNA) is known to vary strongly with the targeted position of the mRNA. A number of hypotheses have been suggested to explain this phenomenon. We would like to test if this positional effect is mainly due to the secondary structure of the mRNA at the target site. We proposed that this structural factor can be characterized by a single parameter called "the hydrogen bond (H-b) index," which represents the average number of hydrogen bonds formed between nucleotides in the target region and the rest of the mRNA. This index can be determined using a computational approach. We tested the correlation between the H-b index and the gene-silencing effects on three genes (Bcl-2, hTF, and cyclin B1) using a variety of siRNAs. We found that the gene-silencing effect is inversely dependent on the H-b index, indicating that the local mRNA structure at the targeted site is the main cause of the positional effect. Based on this finding, we suggest that the H-b index can be a useful guideline for future siRNA design.

Base Composition↗

PubMed1992

Structure, localization and transcriptional properties of two classes of retinoic acid receptor alpha fusion proteins in acute promyelocytic leukemia (APL): structural similarities with a new family of oncoproteins.

Acute promyelocytic leukemia (APL) is due to a chromosomal t(15;17) translocation which involves a novel human gene, Myl, (also named PML) and the retinoic acid (RA) receptor alpha (RAR-alpha) gene. We report here the characterization of Myl and of the reciprocal MylRAR (PMLRAR) and RARMyl (RARPML) fusion transcripts which are found in two classes of APL patients. Myl displays similarities with a new family of proteins of which some members are fused to protooncogenes in the transforming proteins RFP-ret and T18. The speckled nuclear localization of Myl, as well as its sequence homology with the 52 kDa component of the RO/SSA ribonucleoprotein particle, suggest that Myl may be present in a ribonucleoprotein complex. In contrast to both Myl and RAR-alpha whose localization is essentially nuclear in the presence or absence of RA, MylRAR which is largely cytoplasmic in the absence of RA appears to be translocated to the nucleus in the presence of RA. Myl and MylRAR can associate in vitro and this association is mediated by a coiled coil in the Myl sequence. In vivo this association results in a colocalization of Myl and MylRAR which is identical to that of MylRAR alone. Studies of activation of transcription from the promoters of several RA target genes indicate that MylRARs have altered transcription activation properties when compared with RAR-alpha. Most notably, MylRAR represses markedly the activity of some RA target promoters in the absence of RA. Western blot analyses of patient samples show that MylRAR is expressed to a much higher level than wild type RAR-alpha originating from the normal allele. Taken together, these results suggest that MylRAR may interfere in a dominant manner with both Myl and RAR functions.

Alleles↗

PubMed1976

The fine structural localization of S-100 protein in rodent cerebellum.

This report describes the first fine structural locations of S-100 protein in the hamster cerebellum. Innovations in tissue fixation as well as tracer preparation enable localization of S-100 protein to several critical cellular and subcellular sites. Certain neuronal elements, Purkinje cells, contain S-100 protein in both cytoplasm and nucleus. Specific membrane structures including plasma membranes and the nuclear membranes of Purkinje cells are strikingly positive. Localization of S-100 protein to the pericapillary astrocytic endfeet as well as regions of the synapse are of particular biological interest. The clear nuclear localization of the molecule suggests a role in the genetic expression of the developing mammalian brain.

Animals↗

PubMed1991

19F NMR studies of the D-galactose chemosensory receptor. 2. Ca(II) binding yields a local structural change.

The Escherichia coli D-galactose and D-glucose receptor possesses a Ca(II)-binding site closely related in structure and metal-binding characteristics to the eukaryotic EF-hand sites. Only the structure of the Ca(II)-occupied site is known. To investigate the structural change triggered by Ca(II) and Sr(II) binding, we have used 19F NMR to probe five 5-fluorotryptophan (5F-Trp) and seven 3-fluorophenylalanine (3F-Phe) positions in the structure, extending the approach described in the preceding article. Of particular interest were two 5F-Trp residues near the N terminus of the Ca(II) site at positions 127 and 133. Substitution of the larger Sr(II) for Ca(II) triggered 19F NMR frequency shifts of the 5F-Trp127 and -133 resonances, indicating a detectable structural change in the Ca(II) site. In contrast, the three 5F-Trp resonances from distant regions of the structure exhibited no detectable frequency shifts. When the metal was removed from the Ca(II) site, the 5F-Trp127 and -133 frequencies shifted to a new value similar to that observed for free 5F-Trp in aqueous solvent, and this new frequency was a function of the H2O to D2O ratio, indicating that the residues had become solvent exposed. Metal removal yielded small or undetectable frequency shifts for the three distant 5F-Trp resonances and for four of the five resolved 3F-Phe resonances. The allosteric coupling of the metal and sugar binding sites was observed to be slight: depletion of metal ions was observed to reduce the D-galactose affinity of the receptor by 2-fold. Together the results indicate that the structural changes in the Ca(II) site are primarily localized in the region of the site. Removal of the metal ion from the site exposes the nearby 5F-Trp127 and -133 residues to the solvent, suggesting that the empty site has a more open structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Calcium↗