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Local structure of the zeolitic catalytically active site during reaction.

The structural changes of the catalytic active site that occur during catalytic reaction in an acidic zeolite are detected. The local structure of the zeolitic Brønsted active site is a distorted tetrahedrally coordinated aluminum that has three short and one long aluminum-oxygen bond. Using in situ Al K edge X-ray absorption spectroscopy, the adsorption of a reactive intermediate in the oligomerization of ethene changed the local structure of the catalytic active site; the long aluminum oxygen bond is partially relaxed. At increasingly higher temperature, extensive coking of the catalyst frees the Brønsted acid site from the reactive intermediate, restoring the asymmetric coordination. These measurements show that application of in situ Al K edge spectroscopy provides fundamental insight into the structure of zeolitic catalytically active sites during catalytic action.

Journal Article↗

Local structure of beta-hairpin isotopomers by FTIR, 2D IR, and ab initio theory.

The 12-residue tryptophan zipper beta-hairpin (SWTWENGKWTWK) and two (13)C-isotopomers were examined in the amide-I region using FTIR and femtosecond two-dimensional infrared (2D IR) spectroscopies. Spectroscopic features of the labeled transitions with (13)C-substituted amide unit present in the terminal or turn region of the hairpin, including their frequency shifts and distributions, line broadenings, orientations, and anharmonicities of diagonal peaks, allow the peptide local structure and local environment to be examined. The results suggest a larger structure fluctuation in the terminal region than in the turn region as a result of the side chain effect and solvent-peptide interaction. The results also suggest that the uncoupled amide-I modes are not degenerate and that this is likely to be a common situation for solvated polypeptides. In addition, the amide-I states in the terminal and turn regions were found to be delocalized over several neighboring amide units. Cross-peaks between the various labeled and unlabeled structural regions were clearly observed in the 2D IR correlation spectra, allowing them to be characterized for monitoring structural changes. These results illustrate the sensitivity of 2D IR to the local environment of solvated peptides. The simulated 1D and 2D IR spectra of the hairpin, obtained by using the vibrational exciton model incorporating coupling constants from quantum chemical computations and semiempirical calculations, were found to reproduce the essential features of the experimental results.

Amides↗

Local structure evolution of FexNi77-xCu(1-)Nb2P14B6 soft magnetic materials by mechanical alloying.

Mechanically alloyed Fe(x)Ni77-xCu1Nb2P14B6 soft magnetic materials have been prepared with different atomic compositions. The alloy structures are investigated by X-ray absorption fine structure (XAFS). The results show that mechanical alloying (MA) can drive the Fe(x)Ni77-xCu1Nb2P14B6 powder mixture to produce amorphous alloy while the atomic concentration of Fe element is about and over 40%. On the contrary, the MA Fe(x)Ni77 xCu1Nb2P14B6 is a solid solution with a fcc-like structure in the region of lower Fe atomic concentration (<22%), preserving a medium-range order around Ni and Fe atoms. Moreover, we have found that the local structure geometry of Fe atom is similar to that of Ni atom for all the MA Fe(x)Ni77-xCu1NbP14B6 samples. It indicates that the local structures of Fe and Ni atoms in a Fe(x)Ni77-xCu1Nb2P14B6 sample only depend on the x value of element Ni after ball milling.

Journal Article↗

Local structure analyses of Ce0.5Zr0.5O2 mixed oxides by XAFS.

Three types of CeO2-ZrO2 with the same composition (Ce/Zr = 1) were prepared by different methods, exhibited the different oxygen storage/release capacity (OSC). To investigate the relationship between the OSC and the local structure, the Ce and Zr K-edges XAFS spectra for these samples were measured. The features of Fourier transforms of these samples were different from each other. This suggested that the OSC was remarkably exerted by the local structure around Ce and Zr. The quantitative curve-fitting analysis of EXAFS was applied, and it was concluded that homogeneous Ce(0.5)Zr(0.5)O2 solid solution at atomic level exhibited the highest OSC among these CeO2-ZrO2 with the same composition (Ce/Zr = 1).

Journal Article↗

Universal relationship between magnetization and changes in the local structure of La1-xCaxMnO3: evidence for magnetic dimers.

We present extensive x-ray absorption fine structure measurements on La(1-x)Ca(x)MnO(3) as a function of the B field (to 11 T) and Ca concentration, chi(21%-45%). These results reveal local structure changes (associated with polaron formation) that depend only on the magnetization for a given sample, irrespective of whether the magnetization is achieved through a decrease in temperature or an applied magnetic field. Furthermore, the relationship between local structure and magnetization depends on the hole doping. A model is proposed in which a filamentary magnetization initially develops via the aggregation of pairs of Mn atoms involving a hole and an electron site. These pairs have little distortion and it is likely that they form at temperature T(*) above T(c).

Journal Article↗

Assessing local structural perturbations in proteins.

BACKGROUND: Protein structure research often deals with the comparison of two or more structures of the same protein, for instance when handling alternative structure models for the same protein, point mutants, molecule movements, structure predictions, etc. Often the difference between structures is small, restricted to a local neighborhood, and buried in structural "noise" due to trivial differences resulting from experimental artifacts. In such cases, whole-structure comparisons by means of structure superposition may be unsatisfactory and researchers have to perform a tedious process of manually superposing different segments individually and/or use different frames of reference, chosen roughly by educated guessing. RESULTS: We have developed an algorithm to compare local structural differences between alternative structures of the same protein. We have implemented the algorithm through a computer program that performs the numerical evaluation and allows inspecting visually the results of the structure comparison. We have tested the algorithm on different kinds of model systems. Here we present the algorithm and some results to illustrate its characteristics. CONCLUSION: This program may provide an insight into the local structural changes produced in a protein structure by different interactions or modifications. It is convenient for the general user and it can be applied to standard or specific tasks on protein structure research.

Algorithms↗

The local structure of protonated water from x-ray absorption and density functional theory.

We present a combined x-ray absorption spectroscopy/computational study of water in hydrochloric acid (HCl) solutions of varying concentration to address the structure and bonding of excess protons and their effect on the hydrogen bonding network in liquid water. Intensity variations and energy shifts indicate changes in the hydrogen bonding structure in water as well as the local structure of the protonated complex as a function of the concentration of protons. In particular, in highly acidic solutions we find a dominance of the Eigen form, H(3)O(+), while the proton is less localized to a specific water under less acidic conditions.

Journal Article↗

[The task of determining the local structure of proteins by Overhauser effect nuclear spectroscopy addressed once more].

The testing of the earlier developed theoretical method for determining the backbone protein conformations (the local structure) on the basis of the two-dimensional nuclear Overhauser effect (NOE) spectroscopy has been fulfilled. The method approval has been carried out by the calculation (based upon spectral NOE parameters) of the local plastocyanin and bovine pancreatic trypsin inhibitor structures followed by the comparison of the received conformational parameters with the X-ray data. The comparison of the molecular conformations in solution and crystal has been implemented for different fragments of the polypeptide chain (beta-structures, alpha-helices, irregular segments) using the mathematical statistics methods. The verification of the "zero" hypothesis about the similarity of phi and psi variation rows which was carried out at the reliability level of 0.99 showed that in both cases there were no systematic deviations of dihedral angles of the compared conformations and that their dispersion differences were statistically indiscernible. It has been concluded that the approved method permits to determine the local structure of the conformationally rigid proteins (or their fragments) at the level close to that which provides the high resolution X-ray analysis.

Amino Acid Sequence↗

Local-structural diversity and protein folding: application to all-beta off-lattice protein models.

Global measures of structural diversity within a distribution of biopolymers, such as the radius of gyration and percent native contacts, have proven useful in the analysis of simulation data for protein folding. In this paper we describe a statistical-based methodology to quantify the local structural variability of a distribution of biopolymers, applied to 46- and 69-"residue" off-lattice, three-color model proteins. Each folds into beta-barrel structures. First we perform a principal component analysis of all interbead distance variables for a large number of independent, converged Boltzmann-distributed samples of conformations collected at each of a wide range of temperatures. Next, the principal component vectors are subjected to orthogonal (varimax) rotation. The results are displayed on so-called "squared-loading" plots. These provide a quantitative measure of the contribution to the sample variance of the position of each residue relative to the others. Dominant structural elements, those having the largest structural diversity within the sampled distribution, are responsible for peaks and shoulders observed in the specific heat versus temperature curves, generated using the weighted histogram analysis method. The loading plots indicate that the local-structural diversity of these systems changes gradually with temperature through the folding transition but radically changes near the collapse transition temperature. The analysis of the structural overlap order statistic suggests that the 46-mer thermodynamic folding transition involves the native state and at least three other nearly native intermediates. In the case of the 46-mer protein model, data are generated at sufficiently low temperatures that squared-loading plots, coupled with cluster analysis, provide a local and energetic description of its glassy state.

Algorithms↗

Stabilization of local structures by pi-CH and aromatic-backbone amide interactions involving prolyl and aromatic residues.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) and CHn of aliphatic groups (pi-CH) are known to form local structures and to stabilize secondary structure in peptides and proteins. To investigate the existence of these interactions and to explore their possible role in constraining the structures of Pro-Xaa and Xaa-Pro fragments in proteins, a database search was performed in a non-redundant set of proteins from the Brookheaven Protein Data Bank for pi-CH and Ar-HN interactions in Pro-Xaa and Xaa-Pro fragments (where Xaa is either Phe, Tyr or Trp). In Xaa-Pro fragments, the percentage of pi-CH interactions and Ar-HN interactions, respectively, was 20.6 and 3.2%, in Pro-Xaa fragments 26.8, 8.6 and 4.0% of the Pro-Xaa fragments contained both interactions, while no Xaa-Pro fragments had both. The protein fragments containing Ar-HN and/or pi-CH interactions were clustered on the basis of similarity of selected torsion angles. The clustering resulted in well defined clusters. Thus, pi-CH and Ar(i)-HN(i) interactions were able to constrain individual conformations of the Pro-Xaa and Xaa-Pro fragments. These local structures were found to be independent of the secondary structure of the polypeptide chains in which the fragments were found.

Amides↗

Local structures of ions at ion-exchange resin/solution interface.

The local structures of Cl- and Br- in anion-exchange resins have been studied by X-ray absorption fine structure (XAFS), and separation selectivity is discussed on the basis of results. When two different anion-exchange resins having trimethylammonium and dimethylammonium groups as anion-exchange groups are employed for ion-exchange experiments, slightly higher Br- selectivity has been obtained with the former. XAFS has indicated that the average hydration numbers for a given anion is not affected by the structure of the ion-exchange group, but that the extent of ion-association between the anion and the ion-exchange groups depends on the type of the ion-exchange group. Shorter interaction distance (and in turn stronger ion-association) has been confirmed for the dimethylammonium-type resin, and is consistent with lower Br- selectivity of this resin.

Anion Exchange Resins↗

Search for a new description of protein topology and local structure.

A novel description of protein structure in terms of the generalized secondary structure elements (GSSE) is proposed. GSSE's are defined as fragments of the protein structure where the chain doesn't radically change its direction. In this new language, global protein topology becomes a particular arrangement of the relatively small number of large, rod like GSSE's. Protein topology can be described by an adjacency matrix giving information, which GSSE's are close in space to each other and defining a graph, where GSSE's are equivalent to vertices and interactions between them to edges. The information about the local structure is translated into the local density of pseudo-Calpha atoms along the chain and the curvature of the chain. This new description has a number of interesting and useful features. For instance, enumeration theorems of graph theory can be used to estimate a number of possible topologies for a protein built from a given number of elements. Different topologies, including novel ones, can be generated from the known by various permutations of elements. Many new regularities in protein structures become suddenly visible in a new description. A new local structure description is more amenable to predictions and easier to use in fold predictions.

Animals↗

X-ray absorption near-edge spectroscopy of transferrins: a theoretical and experimental probe of the metal site local structure.

Proteins of the transferrin (Tf) family have a role in metal transport in vertebrates and have been extensively studied. The results here reported provide, for the first time, a detailed systematic comparison of metal sites in Tf complexes involving several atoms in the whole protein and in two different types of Tfs. The high interest in the structural variations induced in a metalloprotein upon the uptake of different metals is related to the hypothesis of the metals' involvement in some neuropathologies. We propose a comparative study of the X-ray absorption spectra at the K-edge of iron, copper, zinc and nickel in serotransferrin and ovotransferrin. The experimental data are simulated using an algorithm of the full multiple scattering method. Our results show that: (1) the local structure of each site (N-terminal and C-terminal) is correlated to the ligation state of the other site; (2) the difference between the two proteins is related to site local structure and depends on the metal ion nature being greater in the case of copper and zinc with respect to iron and nickel ions; (3) X-ray spectroscopy is confirmed as a suitable technique able to discriminate between coordination models proposed by X-ray diffraction.

Animals↗

Fine structural localization of arylsulfatase B activity in the rabbit blood platelets.

Fine structural localization of arylsulfatase in the rabbit blood platelets has been investigated in this study. Among many cell organellae, reaction products were exclusively observed in the alpha granules of the platelets. Within the alpha granules, arylsulfatase activity appeared to localize in variable patterns, i.e. reaction products confined mainly at the peripheral region in many granules, while they deposited heavily throughout the granule matrices in some others. In a blood platelets, each alpha granule showed the different staining pattern which indicated more variable functional heterogeneity in the granules.

Animals↗

[Situation and role of local structures of hospital ethics: s survey of Hospital Public Care in Paris].

This article presents the main results of a survey carried out among the local structures for hospital ethics of the Public Assistance sector of the Hospitals of Paris. The results show that the situation of these structures has completely transformed itself since the law of 1988 on human research. Only four ethics committees subsist out of the 16 university-hospital committees that existed in 1991. Seven new structures have been created since 1994, which are open to all categories of personnel and within which doctors are a minority. The four ethics committees provide almost no decision making opinions anymore and are, like the new groups, fora for discussion, reflection, or even information on issues of hospital ethics. Almost none of these structures has an official mission. This situation presents the question of the role that a local ethics structure can hold within a hospital.

Data Collection↗

Analytical approach to localized structures in a simple reaction-diffusion system.

We study from an analytical point of view a simple reaction-diffusion model, which admits stable oscillating localized structures as a consequence of the coexistence between a stable limit cycle and a stable fixed point. Using a generalized matching approach we are able to find approximate analytical expressions for localized oscillating structures in this reaction-diffusion model capturing all the essential ingredients of these breathing particlelike solutions.

Diffusion↗

The Local Structure of Space-variant Images.

Local image structure is widely used in theories of both machine and biological vision. The form of the differential operators describing this structure for space-invariant images has been well documented. Although space-variant coordinates are universally used in mammalian visual systems, the form of the operators in the space-variant coordinate system has received little attention. In this report we derive the form of the most common differential operators and surface characteristics in the space-variant domain and show examples of their use. The operators include the Laplacian, the gradient and the divergence, as well as the fundamental forms of the image treated as a surface. We illustrate the use of these results by deriving the space-variant form of corner detection and image enhancement algorithms. The latter is shown to have interesting properties in the complex log domain, implicitly encoding a variable grid-size integration of the underlying PDE, allowing rapid enhancement of large scale peripheral features while preserving high spatial frequencies in the fovea. Copyright 1997 Elsevier Science Ltd.

Journal Article↗

Local structure of guest molecules in gas hydrates--a model study of Kr and Xe clathrates.

Gas hydrates constitute a class of solids in which small molecules occupy cavities inside an ice-like structure. There is enormous scientific and technological interest in understanding the structure, stability and formation mechanism of clathrates. We developed and constructed a variable temperature high-pressure cell for x-rays measurements, which allows in situ studies of clathrate formation or decomposition. We used XAFS and Diffraction techniques to study the evolution of the structure during formation and decomposition. We studied two clathrates structures, structure I (Xe) and structure II (Kr). We were able to identify the local structure around the guest atom. We identified the rare gas-water complexes that act as precursor to the formation of the crystalline phases. We observed the transformation of the clathrate from structure II to structure I when Xe is added to Kr clathrates.

Journal Article↗