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At least 703 records · Page 39Linked to original sources
PubMed2005

Local electronic structure of single-walled carbon nanotubes from electrostatic force microscopy.

An atomic force microscope was used to locally perturb and detect the charge density in carbon nanotubes. Changing the tip voltage varied the Fermi level in the nanotube. The local charge density increased abruptly whenever the Fermi level was swept through a van Hove singularity in the density of states, thereby coupling the cantilever's mechanical oscillations to the nanotube's local electronic properties. By using our technique to measure the local band gap of an intratube quantum-well structure, created by a nonuniform uniaxial strain, we have estimated the nanotube chiral angle. Our technique does not require attached electrodes or a specialized substrate, yielding a unique high-resolution spectroscopic tool that facilitates the comparison between local electronic structure of nanomaterials and further transport, optical, or sensing experiments.

Electrochemistry↗
PubMed2004

Front dynamics in an oscillatory bistable Belousov-Zhabotinsky chemical reaction.

We observe breathing front dynamics which select three distinct types of bistable patterns in the 2:1 resonance regime of the periodically forced oscillatory Belousov-Zhabotinsky reaction. We measure the curvature-driven shrinking of a circular domain R approximately t(1/2) at forcing frequencies below a specific value, and show that the fast time scale front oscillations (breathing) drive this slow time scale shrinking. Above a specific frequency, we observe fronts of higher curvature grow instead of shrink and labyrinth patterns form. Just below the transition frequency is a relatively narrow range of frequencies where the curvature-driven coarsening is balanced by a competing front interaction, which leads to a pattern of localized structures. The length scale of the localized structure and labyrinth patterns is set by the front interactions.

Journal Article↗
PubMed2005

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

BACKGROUND: MicroRNAs (miRNAs) are a group of short (approximately 22 nt) non-coding RNAs that play important regulatory roles. MiRNA precursors (pre-miRNAs) are characterized by their hairpin structures. However, a large amount of similar hairpins can be folded in many genomes. Almost all current methods for computational prediction of miRNAs use comparative genomic approaches to identify putative pre-miRNAs from candidate hairpins. Ab initio method for distinguishing pre-miRNAs from sequence segments with pre-miRNA-like hairpin structures is lacking. Being able to classify real vs. pseudo pre-miRNAs is important both for understanding of the nature of miRNAs and for developing ab initio prediction methods that can discovery new miRNAs without known homology. RESULTS: A set of novel features of local contiguous structure-sequence information is proposed for distinguishing the hairpins of real pre-miRNAs and pseudo pre-miRNAs. Support vector machine (SVM) is applied on these features to classify real vs. pseudo pre-miRNAs, achieving about 90% accuracy on human data. Remarkably, the SVM classifier built on human data can correctly identify up to 90% of the pre-miRNAs from other species, including plants and virus, without utilizing any comparative genomics information. CONCLUSION: The local structure-sequence features reflect discriminative and conserved characteristics of miRNAs, and the successful ab initio classification of real and pseudo pre-miRNAs opens a new approach for discovering new miRNAs.

Animals↗
PubMed2005

Finding local community structure in networks.

Although the inference of global community structure in networks has recently become a topic of great interest in the physics community, all such algorithms require that the graph be completely known. Here, we define both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time. This algorithm runs in time O(k2d) for general graphs when d is the mean degree and k is the number of vertices to be explored. For graphs where exploring a new vertex is time consuming, the running time is linear, O(k). We show that on computer-generated graphs the average behavior of this technique approximates that of algorithms that require global knowledge. As an application, we use this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer.

Journal Article↗
PubMed2004

Multiple scattering x-ray absorption studies of Zn2+ binding sites in bacterial photosynthetic reaction centers.

Binding of transition metal ions to the reaction center (RC) protein of the photosynthetic bacterium Rhodobacter sphaeroides has been previously shown to slow light-induced electron and proton transfer to the secondary quinone acceptor molecule, Q(B). On the basis of x-ray diffraction at 2.5 angstroms resolution a site, formed by AspH124, HisH126, and HisH128, has been identified at the protein surface which binds Cd(2+) or Zn(2+). Using Zn K-edge x-ray absorption fine structure spectroscopy we report here on the local structure of Zn(2+) ions bound to purified RC complexes embedded into polyvinyl alcohol films. X-ray absorption fine structure data were analyzed by combining ab initio simulations and multiparameter fitting; structural contributions up to the fourth coordination shell and multiple scattering paths (involving three atoms) have been included. Results for complexes characterized by a Zn to RC stoichiometry close to one indicate that Zn(2+) binds two O and two N atoms in the first coordination shell. Higher shell contributions are consistent with a binding cluster formed by two His, one Asp residue, and a water molecule. Analysis of complexes characterized by approximately 2 Zn ions per RC reveals a second structurally distinct binding site, involving one O and three N atoms, not belonging to a His residue. The local structure obtained for the higher affinity site nicely fits the coordination geometry proposed on the basis of x-ray diffraction data, but detects a significant contraction of the first shell. Two possible locations of the second new binding site at the cytoplasmic surface of the RC are proposed.

Absorptiometry, Photon↗
PubMed2004

Local atomic structures of palladium nanowire.

In this paper, investigation of the structure of palladium nanowire has been performed by using genetic algorithm simulation based on the molecular dynamics. Our calculation employs a well-fitted, tight-binding many-body potential for Pd atoms. Some local atomic structures and defects in nanowires have been reported. The melting behavior of palladium nanowire has also been investigated. An interesting result is that the diffusion of the central atoms results in the beginning of the melting. The moving central atoms build up a monostrand atomic chain during the melting process. The single atomic chain is very stable which can exist in a wide temperature region (800-950 K). The formation of the single atomic chain causes some new defects in the nanowire. And the new defects result in the decrease of the thermal stability of the nanowire. Interestingly, the liquid from the nanowire melting has a supercooled feature because the splitting of the second peak of pair correlation function is observed. The curves of the internal energy and the local cluster are used to monitor the phase transition. The melting of the nanowire is not only due to the single atomic diffusion, but also the diffusion of the local clusters.

Journal Article↗
PubMed2001

Structure, chromosomal localization, and expression of the gene for mouse ecto-mono(ADP-ribosyl)transferase ART5.

Mono(ADP-ribosyl)transferases regulate the function of target proteins by attaching ADP-ribose to specific amino acid residues in their target proteins. The purpose of this study was to determine the structure, chromosomal localization, and expression profile of the gene for mouse ecto-ADP-ribosyltransferase ART5. Southern blot analyses indicate that Art5 is a single copy gene which maps to mouse chromosome 7 at offset 49.6 cM in close proximity to the Art1, Art2a and Art2b genes. Northern blot and RT-PCR analyses demonstrate prominent expression of Art5 in testis, and lower levels in cardiac and skeletal muscle. Sequence analyses reveal that the Art5 gene encompasses six exons spanning 8 kb of genomic DNA. The 5' end of the Art5 gene overlaps with that of the Art1 gene. A single long exon encodes the predicted ART5 catalytic domain. Separate exons encode the N-terminal leader peptide and a hydrophilic C-terminal extension. Sequencing of RT-PCR products and ESTs identified six splice variants. The deduced amino acid sequence of ART5 shows 87% sequence identity to its orthologue from the human, and 37 and 32% identity to its murine paralogues ART1 and ART2. Unlike ART1 and ART2, ART5 lacks a glycosylphosphatidylinositol-anchor signal sequence and is predicted to be a secretory enzyme. This prediction was confirmed by transfecting an Art5 cDNA expression construct into Sf9 insect cells. The secreted epitope-tagged ART5 protein resembled rat ART2 in exhibiting potent NAD-glycohydrolase activity. This study provides important experimental tools to further elucidate the function of ART5.

ADP Ribose Transferases↗
PubMed1991

Mechanism of protein folding. II. Lysozyme and phospholipase.

Refolding of hen egg-white lysozyme assuming the formation of secondary structures (alpha-helices and beta-sheets) is carried out by the method presented in the previous paper (N. Saitô et al., Proteins; Struct. Funct. Genet. 3 (1988) 199-208). To do this, the hydrophobic interactions between the hydrophobic residues which are located at the key positions for folding and can be identified without the knowledge of the native structure, and the nonbonded interactions between every pair of atoms (except hydrogen) or groups are introduced successively from short- to medium-distance pairs. The search for the energy minimum by these interactions can afford a conformation of especially the mutual arrangements between neighboring secondary structures. When these local structures are accomplished, some of the long-distance amino-acid pairs come close together and then the possible interactions (hydrophobic, nonbonded) are introduced. The three-dimensional structure of lysozyme thus obtained is shown to have locally correct arrangements of the secondary structures, but mutual relations between long-distance parts of the chain are not similar to the native structure. The introduction of disulfide bonds between appropriate cysteine residues is necessary to reach the native structure. The choice of cysteine pairs for disulfide bonding is made by the criterion given in the paper to follow (K. Watanabe, A. Nakamura, Y. Fukuda and N. Saitô. Biophys. Chem. 40 (1991) 293). The same treatment is applied to bovine pancreatic phospholipase with 7 disulfide bonds. The formation of the antiparallel beta-structures from neighboring beta-strands and the problem of the folding order are also discussed.

Amino Acid Sequence↗
PubMed1982

Correlation between ventral surface structures and local degeneration of cilia during conjugation in Paramecium.

Correlation between cortical structures, such as the suture lines and the oral apparatus, and local degeneration of cilia during conjugation was investigated using aberrantly shaped cells which were produced by treating normal cells with 2 mM adenine for 24 h. Three types of aberrantly shaped cells were obtained: (1) proters, in which the oral apparatus is located at or near the posterior end of the cell and the preoral suture is much longer than that of a normally shaped cell' (2) opisthes, in which the oral apparatus is located extremely anteriorly, the preoral suture is very short and bent to the left, and the postoral suture and cytoproct are much longer than those of normally shaped cells; and (3) L-shaped cells, which are cells that have not separated at division and contain two buccal openings. The anterior member of the L-shaped cells (AML) has a long preoral suture and the posterior member of the L-shaped cell (PML) has a long postoral suture and cytoproct. The postoral field of AML and the preoral field of PML are missing. When these cells were mixed with normally shaped cells of the opposite mating type, the mating reaction took place between them. Scanning electron microscopic observation showed that, in all abnormally shaped cells, the degeneration of cilia always occurred along the full length of the preoral suture, regardless of its total length, and along the posterior right field of the buccal vestibulum, regardless of its location in the cell cortex. The localization of the degeneration of cilia, therefore, coincided with the position of the preoral suture and the buccal opening.

Adenine↗
PubMed2005

Effect of protein structure on mitochondrial import.

Most proteins that are to be imported into the mitochondrial matrix are synthesized as precursors, each composed of an N-terminal targeting sequence followed by a mature domain. Precursors are recognized through their targeting sequences by receptors at the mitochondrial surface and are then threaded through import channels into the matrix. Both the targeting sequence and the mature domain contribute to the efficiency with which proteins are imported into mitochondria. Precursors must be in an unfolded conformation during translocation. Mitochondria can unfold some proteins by changing their unfolding pathways. The effectiveness of this unfolding mechanism depends on the local structure of the mature domain adjacent to the targeting sequence. This local structure determines the extent to which the unfolding pathway can be changed and, therefore, the unfolding rate increased. Atomic force microscopy studies find that the local structures of proteins near their N and C termini also influence their resistance to mechanical unfolding. Thus, protein unfolding during import resembles mechanical unfolding, and the specificity of import is determined by the resistance of the mature domain to unfolding as well as by the properties of the targeting sequence.

Microscopy, Atomic Force↗
PubMed2006

Fluorescence X-ray absorption spectroscopy using a Ge pixel array detector: application to high-temperature superconducting thin-film single crystals.

A Ge pixel array detector with 100 segments was applied to fluorescence X-ray absorption spectroscopy, probing the local structure of high-temperature superconducting thin-film single crystals (100 nm in thickness). Independent monitoring of pixel signals allows real-time inspection of artifacts owing to substrate diffractions. By optimizing the grazing-incidence angle theta and adjusting the azimuthal angle phi, smooth extended X-ray absorption fine structure (EXAFS) oscillations were obtained for strained (La,Sr)2CuO4 thin-film single crystals grown by molecular beam epitaxy. The results of EXAFS data analysis show that the local structure (CuO6 octahedron) in (La,Sr)2CuO4 thin films grown on LaSrAlO4 and SrTiO3 substrates is uniaxially distorted changing the tetragonality by approximately 5 x 10(-3) in accordance with the crystallographic lattice mismatch. It is demonstrated that the local structure of thin-film single crystals can be probed with high accuracy at low temperature without interference from substrates.

Algorithms↗
PubMed2006

Molecular flexibility in protein-DNA interactions.

In living cells protein-DNA interactions are fundamental processes. Here, we compare the 3D structures of several DNA-binding proteins frequently determined with and without attached DNA. We studied the global structure (backbone-traces) as well as the local structure (binding sites) by comparing pair-wise the related atoms. The DNA-interaction sites of uncomplexed proteins show conspicuously high local structural flexibility. Binding to DNA results in specific local conformations, which are clearly distinct from the unbound states. The adaptation of the protein's binding site to DNA can never be described by the lock and key model but in all cases by the induced fit model. Conformational changes in the seven protein backbone traces take place in different ways. Two of them dock onto DNA without a significant change, while the other five proteins are characterized by a backbone conformation change caused by DNA docking. In the case of three proteins of the latter group the DNA-complexed conformation also occurs in a few uncomplexed structures. This behavior can be described by a conformational ensemble, which is narrowed down by DNA docking until only one single DNA-complexed conformation occurs. Different docking models are discussed and each of the seven proteins is assigned to one of them.

Binding Sites↗
PubMed2004

Local backbone structure prediction of proteins.

A statistical analysis of the PDB structures has led us to define a new set of small 3D structural prototypes called Protein Blocks (PBs). This structural alphabet includes 16 PBs, each one is defined by the (phi, psi) dihedral angles of 5 consecutive residues. The amino acid distributions observed in sequence windows encompassing these PBs are used to predict by a Bayesian approach the local 3D structure of proteins from the sole knowledge of their sequences. LocPred is a software which allows the users to submit a protein sequence and performs a prediction in terms of PBs. The prediction results are given both textually and graphically.

Amino Acid Sequence↗
PubMed2005

Local electronic structure of layered Li(x)Ni0.5Mn0.5O2 and Li(x)Ni(1/3)Mn(1/3)Co(1/3)O2.

Samples of Li(x)Ni0.5Mn0.5O2 and Li(x)Ni(1/3)Mn(1/3)Co(1/3)O2 were prepared as active materials in electrochemical half-cells and were cycled electrochemically to obtain different values of Li concentration, x. Absorption edges of Ni, Mn, Co, and O in these materials of differing x were measured by electron energy loss spectrometry (EELS) in a transmission electron microscope to determine the changes in local electronic structure caused by delithiation. The work was supported by electronic structure calculations with the VASP pseudopotential package, the full-potential linear augmented plane wave code WIEN2K, and atomic multiplet calculations that took account of the electronic effects from local octahedral symmetry. A valence change from Ni2+ to Ni4+ with delithiation would have caused a 3 eV shift in energy of the intense white line at the Ni L3 edge, but the measured shift was less than 1.2 eV. The intensities of the "white lines" at the Ni L-edges did not change enough to account for a substantial change of Ni valence. No changes were detectable at the Mn and Co L-edges after delithiation either. Both EELS and the computational efforts showed that most of the charge compensation for Li+ takes place at hybridized O 2p states, not at Ni atoms.

Journal Article↗
PubMed1988

Trophoblast-specific beta 1-glycoprotein: its spatial structure and localization of antigenic determinants.

Effects of temperature and pH on the spatial structures of trophoblast-specific beta 1-glycoprotein (TSG) and its various derivatives and fragments have been studied by circular dichroic spectroscopy. The spatial organization of the protein portion of TSG derivatives, as revealed by the spectroscopic evidence, has been discussed with respect to the antigenic activity of the species studied. We concluded that the TSG protein portion consists mainly of a beta-structural type. The antigenic determinants were shown to be topographic, and are preferentially localized in the protein portion; only about 15% of the TSG antigenic activity failed to bear a direct relation to the spatial structure. The antigenic determinants seemed to include a tryptophan residue.

Circular Dichroism↗
PubMed1987

Effects of the coherence of illumination on electron microdiffraction pattern intensities.

Microdiffraction is capable of revealing the local structure within an area of the specimen consisting of only a few, or a few tens of, unit cells. However, the extent to which the diffraction pattern intensities can show the local structure depends strongly on the coherence of the illumination. If the coherence width of the illumination is smaller than the diameter of the electron probe at the specimen level, the details within the diffraction spots, which indicate deviations of the local structure from the periodicity of the crystal, will be lost. The differences in the amount of spot splitting observed in microdiffraction patterns from out-of-phase domain boundaries, observed with two instruments, are attributed to differences in the effective source sizes.

Computer Simulation↗
PubMed2006

Local electronic structure of near oxygen dopants: a window on the high-Tc pairing mechanism.

The cuprate material (Bi(2)Sr(2)CaCu(2)O-2212) is believed to be doped by a combination of cation switching and excess oxygen. The interstitial oxygen dopants are of particular interest because scanning tunneling microscopy (STM) experiments have shown that they are positively correlated with the local value of the superconducting gap, and calculations suggest that the fundamental attraction between electrons is modulated locally. In this work, we use density functional theory to try to ascertain which locations in the crystal are energetically most favorable for the O dopant atoms, and how the surrounding cage of atoms deforms. Our results provide support for the identification of STM resonances at -1 with dopant interstitial O atoms, and show how the local electronic structure is modified nearby.

Journal Article↗
PubMed2003

Supertargeted chemistry: identifying relationships between molecular structures and their sub-cellular distribution.

Supertargeted chemistry is the study of how chemical structures localize or direct molecules to specific sub-cellular compartments in living cells. Supertargeting can be used to increase the activity or specificity of an inhibitor against its target, by concentrating the inhibitor in the particular organelle where the target is active. But, unlike structure-activity relationships, structure-localization relationships are not a simple function of compound concentration. Various aspects of mitochondrial physiology, proteomics and pharmacology have made this the organelle of choice for supertargeting studies. While exploration of supertargeting strategies to this and the other organelles has been limited, combinatorial chemical libraries of fluorescent molecules are beginning to illuminate new supertargeting mechanisms at the sub-cellular level. Moreover, predictive approaches that determine the relationship between a molecule's features and sub-cellular localization are being developed in the related field of functional genomics. Applied to the small molecules, such strategies could prove useful for predicting structure-localization relationships amongst large libraries of compounds.

Animals↗