Theoretical study of grain boundaries in Si: Effects of structural disorder on the local electronic structure and the origin of band tails.
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Journal Article↗
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Emergence of non-random structure in local food webs generated from randomly structured regional webs.
Previous studies have shown that high-resolution, empirical food webs possess a non-random network structure, typically characterized by uniform or exponential degree distributions. However, the empirical food webs that have been investigated for their structural properties represent local communities that are only a subset of a larger pool of regionally coexisting species. Here, we use a simple model to investigate the effects of regional food web structure on local food webs that are assembled by two simple processes: random immigration of species from a source web (regional food web), and random extinction of species within the local web. The model shows that local webs with non-random degree distributions can arise from randomly structured source webs. A comparison of local webs assembled from randomly structured source webs with local webs assembled from source webs generated by the niche model shows that the former have higher species richness at equilibrium, but have a nonlinear response to changing extinction rates. These results imply that the network structure of regional food webs can play a significant role in the assembly and dynamics of local webs in natural ecosystems. With natural landscapes becoming increasingly fragmented, understanding such structure may be a necessary key to understanding the maintenance and stability of local species diversity.
Animals↗
Cross-level analysis of the influence of local union structure on women's and men's union commitment.
The authors tested the influence of structural features of local unions (N = 43) on members' union commitment (N = 539) as moderated by members' gender. By using a cross-level analysis, they identified local structure with officers' ratings of innovation, formalization, and centralization. An anticipated interaction between gender and innovation was not found. However, as predicted, women's commitment was positively related to formalization and negatively related to centralization. In contrast, men's commitment was only slightly influenced by local formalization but was positively related to centralization. The need for structural redesign to enhance member's commitment, particularly among women, was discussed.
Female↗
Capacitance XAFS method: X-ray absorption spectroscopy of low-dimensional structures.
For local structure analyses of low-dimensional structures in semiconductors, such as defects, interfaces and surfaces, a new site-selective x-ray absorption fine structure (XAFS) measurement, 'capacitance XAFS method', is presented. This method measures the x-ray photon energy dependence of the capacitance involved in diode structures. Since the capacitance is changed by an x-ray induced photoemission of localized electrons in the low dimensional structures, a site-selective analysis can be made. Although macroscopic x-ray absorption can be measured by conventional XAFS analyses, low-dimensional x-ray absorption coefficients are observed by the capacitance XAFS measurements.
Journal Article↗
A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins.
Comparative modeling methods can consistently produce reliable structural models for protein sequences with more than 25% sequence identity to proteins with known structure. However, there is a good chance that also sequences with lower sequence identity have their structural components represented in structural databases. To this end, we present a novel fragment-based method using sets of structurally similar local fragments of proteins. The approach differs from other fragment-based methods that use only single backbone fragments. Instead, we use a library of groups containing sets of sequence fragments with geometrically similar local structures and extract sequence related properties to assign these specific geometrical conformations to target sequences. We test the ability of the approach to recognize correct SCOP folds for 273 sequences from the 49 most popular folds. 49% of these sequences have the correct fold as their top prediction, while 82% have the correct fold in one of the top five predictions. Moreover, the approach shows no performance reduction on a subset of sequence targets with less than 10% sequence identity to any protein used to build the library.
Amino Acid Sequence↗
Structure and localization of mouse Pmscl1 and Pmscl2 genes.
Sera from some patients with polymyositis-scleoderma overlap syndrome (PM-SCL) recognize two antigenically unrelated proteins, PMSCL1 and PMSCL2. Complete mouse Pmscl1 and Pmscl2 cDNA sequences, chromosomal localizations, exon/intron structure, and promoter region sequences of the mouse Pmscl2 gene are presented. The PMSCL1 gene was found to overlap significantly with cyclin A2 in both human and mouse. As such, it may be deduced that PMSCL1 sequences map to human chromosome 4q27 and the proximal portion of mouse chromosome (Chr) 3 where human and mouse cyclin A2 genes reside. Analysis of human and mouse PMSCL1 cDNA sequences provides evidence that the PMSCL1 protein is 68 amino acids longer than previously thought. A BAC containing mouse Pmscl2 was localized to distal mouse Chr 4 by FISH. This BAC contains the microsatellite D4Mit310. D4Mit310 colocalizes with a number of genes that map to human 1p36. In fact, a STS (G25404) located 54.6 cR from the top of human chromosome 1 was found to contain PMSCL2 sequence upon BLAST search.
5' Untranslated Regions↗
CP/MAS 13C NMR characterization of the isomeric states and intermolecular packing in tris(8-hydroxyquinoline) aluminum(III) (Alq3).
The isomeric states and intermolecular packing of tris(8-hydroxyquinoline) aluminum(III) (Alq(3)) in the alpha-, gamma-, and delta-crystalline forms and in the amorphous state, which are important for understanding the light-emitting and electron-transport properties, have been analyzed by CP/MAS (13)C NMR. This simple NMR experiment shows that the isomeric state of alpha- and amorphous Alq(3) is meridional, whereas that of gamma- and delta-Alq(3) is facial. In the amorphous Alq(3), the inclusion of facial isomers has been under debate. Our experiments show that meridional isomers are dominant in the amorphous Alq(3), although the existence of facial isomers cannot be completely denied. The local structure of amorphous Alq(3) is similar to that of alpha-Alq(3) and is significantly different from those of gamma- and delta-Alq(3). Among these Alq(3) samples, the effect of intermolecular interaction is not found only for gamma-Alq(3). This finding can explain the good solvent solubility of gamma-Alq(3), compared with the other crystalline forms. It is also shown that the structures are locally disordered not only for amorphous Alq(3) but also for alpha-Alq(3), although clear X-ray diffraction peaks are observed for alpha-Alq(3). In contrast, the local structures of gamma- and delta-Alq(3) are well defined. A clear relation is found between the spectral patterns of CP/MAS (13)C NMR and the fluorescence wavelengths; the samples, which consist of facial isomers, show blue-shifted fluorescence compared with those of meridionals.
Journal Article↗
Local atomic structure and discommensurations in the charge density wave of CeTe3.
The local structure of in the incommensurate charge density wave (IC-CDW) state has been obtained using atomic pair distribution function analysis of x-ray diffraction data. Local atomic distortions in the Te nets due to the CDW are larger than observed crystallographically, resulting in distinct short and long Te-Te bonds. Observation of different distortion amplitudes in the local and average structures is explained by the discommensurated nature of the CDW, since the pair distribution function is sensitive to the local displacements within the commensurate regions, whereas the crystallographic result averages over many discommensurated domains. The result is supported by STM data. This is the first quantitative local structural study within the commensurate domains in an IC-CDW system.
Journal Article↗
Blind predictions of local protein structure in CASP2 targets using the I-sites library.
Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence--structure motifs, revealing strengths and weaknesses in this new knowledge-based method. Many turns between secondary structural elements were accurately predicted. Estimates of the confidence of prediction correlated well with the accuracy over the whole set. Bias toward structures used to develop the library was minimal, probably because of the extensive use of cross-validation. However, helix positions were better predicted by the PHD program. The method is likely to be sensitive to the quality of the sequence alignment. A general measure for evaluating local structure predictions is suggested.
Binding Sites↗
Diffraction anomalous fine structure of forbidden Bragg reflections: charge localization and structure of the octahedral site in magnetite.
Resonant X ray scattering has been used to investigate charge localization on the octahedral iron atoms in magnetite below and above the Verwey temperature. We have measured the DAFS spectra of the 002 and 006 "forbidden" Bragg reflections permitted by the anisotropy of the iron anomalous scattering factor. We performed ab initio calculations which are in fair agreement with the experiment in the near edge region and demonstrate the sensitivity of the DAFS spectra to tiny structural and electronic changes. No change is observed, in the energy and azimuthal dependences, when the sample is cooled down below the Verwey temperature. Charge ordering can be definitely excluded and different charge localisation schemes discarded. Ab initio simulations, performed by using the refined crystallographic structure proposed for the room temperature phase, do not show a good agreement with the experiment in the extended region of the DAFS spectrum. This point is being investigated.
Journal Article↗
An ab initio study of amide proton shift tensor dependence on local protein structure.
Ab initio shielding tensor calculations were carried out on residues in human ubiquitin. Reported experimental data on isotropic and anisotropic components of the amide proton chemical shifts were used as benchmarks to test the validity of the chosen basis sets as well as methods in structure optimization and shielding calculations. The best agreement with the experimental values was observed when the 6-311**G and 6-311++G(2d,2p) basis sets were used to optimize the structure and to calculate the shielding tensor, respectively. The same method was employed in subsequent model calculations to characterize the dependence of amide proton shielding to the local structure. Both the isotropic and the anisotropic components of the symmetric tensor were found to depend very strongly on the hydrogen bond length. A weaker dependence can also be observed for the hydrogen bond angle. Antisymmetric tensor elements were found to be relatively small. This study permits separation of various local structure contributions to the amide proton shielding tensor that complements scarce experimental data.
Humans↗
An approach to systematic detection of protein structural motifs.
A procedure to detect similar local structures of proteins from C alpha coordinates is presented. First, the conformations of seven-residue peptide segments are approximated by a limited number of representatives, each of which is assigned a symbol. Thus, the overall conformation of a protein is represented by a symbol string. The comparison of these symbol strings using a sequence alignment technique then gives pairs of similar local structures. These pairs are considered candidates of structural motifs. The application of the procedure to the analysis of 93 proteins gave 858 pairs of similar local structures, which included several well-known structural motifs such as the nucleotide-binding beta alpha beta-unit and the calcium-binding EF hand. The characterization of amino acid patterns of similar local structures given by the procedure should be useful for the development of protein structure prediction based on the acquisition of empirical rules from a large-scale database.
Algorithms↗
The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment.
We present an efficient and sensitive hybrid algorithm for local structure alignment of a pair of 3D protein structures. The hybrid algorithm employs both the URMS (unit-vector root mean squared) metric and the RMS metric. Our algorithm searches efficiently the transformation space using a fast screening protocol; initial transformations (rotations) are identified using the URMS algorithm. These rotations are then clustered and an RMS-based dynamic programming algorithm is invoked to find the maximal local similarities for representative rotations of the clusters. Statistical significance of the alignments is estimated using a model that accounts for both the score of the match and the RMS. We tested our algorithm over the SCOP classification of protein domains. Our algorithm performs very well; its main advantages are that (1) it combines the advantages of the RMS and the URMS metrics, (2) it searches extensively the transformation space, (3) it detects complex similarities and structural repeats, and (4) its results are symmetric. The software is available for download at biozon.org/ftp/software/urms/.
Algorithms↗
The effect of global compaction on the local secondary structure of folded dendrimers.
The effect of nonlocal interactions on the local structural propensities of folded dendrimers was evaluated in this work by comparing, under identical conditions, the conformational properties of isomeric dendrimers differing in their global packing efficiency. Accordingly, a modular synthesis of two series of dendrimers up to the third generation was developed to provide efficient access to isomeric dendrimers displaying different levels of overall compaction. Dendrimer compaction levels were adjusted by connecting the folded dendrons to 1,3,5-benzenetricarbonyl chloride, as the central core, via either a 2- or a 4-aminobenzamide linkage to induce relatively "compacted" or "expanded" conformations, respectively. The hydrodynamic volumes of the dendrimers were measured by time-resolved fluorescence anisotropy (TRFA) measurements as a function of the dendrimer series, generation level, and solvent. Packing efficiencies (compaction levels) were estimated by the ratio (V(h)/V(vw)) of the experimental hydrodynamic volume (V(h)) to the calculated van der Waals volume (V(vw)). The extent and stability of local helical bias was measured using circular dichroism and correlated with the packing efficiency (V(h)/V(vw)). These studies suggested that compaction plays an extremely important role in determining the secondary structural preferences of the dendrimers; however, the nature of compaction was more important than the extent of compaction.
Journal Article↗
Annual variation of the angular distribution of the UV beneath public shade structures.
Local governments provide many shade structures at parks and sporting ovals for public use. However, the question remains of how effective are public shade structures at reducing biologically effective UV radiation throughout the year? Broadband measurements of the angular distribution of scattered UV beneath three specific public shade structures was conducted for relatively clear skies and for a solar zenith angle (SZA) ranging from 13 degrees to 76 degrees. The ultraviolet protection factors (UPF) for the shade structures ranged from 18.3 to 1.5 for an increasing SZA. Measurements showed that the horizontal plane received the highest SUV levels from the SZA of 28 degrees to 75 degrees, 42 degrees to 76 degrees, and 50 degrees to 76 degrees for the small, medium and large structures, respectively. This was due to the angle of the sun causing the shade created by the shade structure to be outside the structure. For the small shade structure, the measurements directed to the west were the highest levels in the shade after approximately 28 degrees. For the medium and large shade structures, the measurements directed to the west and south were the highest levels in the shade after roughly 42 degrees and 50 degrees, respectively.
Diffusion↗
Chromatin, DNA methylation and neuron gene regulation--the purpose of the package.
The accessibility of cognate binding sites within a gene promoter can be modified by the condensation or relaxation of local chromatin structure. Local chromatin structure is in turn programmed by covalent modifications of cytosine bases in DNA and amino acid residues in histone protein tails. These chemical and physical adaptations around gene promoters can significantly change levels of mRNA expression. Furthermore, linear patterns of covalent modification of histone protein tails are emerging as a distinct regulatory code--another form of cellular memory. Because chromatin structure can be modified by conventional pharmacologic therapy, a novel approach to the regulation of neuronal gene expression in clinical populations is possible.
Binding Sites↗
Local image structures and optic flow estimation.
Different kinds of local image structures (such as homogeneous, edge-like and junction-like patches) can be distinguished by the intrinsic dimensionality of the local signals. Intrinsic dimensionality makes use of variance from a point and a line in spectral representation of the signal in order to classify it as homogeneous, edge-like or junction-like. The concept of intrinsic dimensionality has been mostly exercised using discrete formulations; however, recent work has introduced a continuous definition. The current study analyzes the distribution of local patches in natural images according to this continuous understanding of intrinsic dimensionality. This distribution reveals specific patterns than can be also associated to local image structures established in computer vision and which can be related to orientation and optic flow features. In particular, we link quantitative and qualitative properties of optic-flow error estimates to these patterns. In this way, we also introduce a new tool for better analysis of optic flow algorithms.
Algorithms↗
Is there a place for local anesthetics structurally different from classical amid or ester local anesthetics?
PURPOSE OF REVIEW: The aim of this review is to describe the pharmacology, toxicology and chemistry of the new group of local anesthetics of phenylcarbamic acid type. RECENT FINDINGS: Basic esters of alkoxy-substituted phenylcarbamic acid have shown high local anesthetic potency, while maintaining a relatively safe toxicity profile. Their potency uniquely increases with the decreasing pH of the external medium. This is of importance when using local anesthesics in inflamed tissues, where the action of common local anesthetics is often problematic. SUMMARY: The most potent phenylcarbamic anesthetics exceed the potency of the most common clinically used local anesthetics 100-300 times. Due to the unique pH dependency of these local anesthetics, further study of their action is required.
Amides↗