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At least 163 records · Page 9Linked to original sources
PubMed2004

Ab initio molecular dynamics simulations of local structure of supercooled Ni.

We report results of first-principles molecular dynamics simulations for stable and undercooled nickel liquids. The calculated structure factors as a function of temperature are discussed with respect to recent experimental measurements. In addition, structural analysis using bonding orientational order and three-dimensional pair analysis techniques have been performed in detail and the effect of undercooling on the microstructure has been analyzed. More particularly, we show the importance of fivefold symmetry local structures.

Journal Article↗
PubMed1996

Formation and control of localized structures in nonlinear optical systems.

Diffractive effects in passive nonlinear optical resonators can lead to pattern-forming instabilities. When the pattern (in our case, a regular hexagonal lattice of intensity peaks) coexists with the homogeneous solution, soliton-like intensity peaks in the transverse plane can be excited. These solutions have the characteristics of localized structures and are highly degenerate with respect to the peak location. By injecting narrow laser pulses, it is possible to turn on such peaks at desired locations and to turn them off selectively. The conditions to ensure independence among the peaks are described as well. These features suggest the possibility of encoding optical information in the structure of the field profile. (c) 1996 American Institute of Physics.

Journal Article↗
PubMed2005

Cascading third-order Raman process and local structure formation in binary liquid mixtures of benzene and n-hexane.

The cascading third-order Raman process in binary mixtures of benzene and n-hexane was studied by six-wave mixing coherent anti-Stokes Raman scattering spectroscopy. By examining the concentration dependence of the cascading third-order signal intensity, we investigated the formation of local structures of benzene in the binary mixtures. A significant deviation from the dependence expected for homogeneous mixtures was observed at benzene concentrations above 7 mol dm(-3). This deviation can be interpreted in terms of optical inhomogeneity caused by the formation of domain structures of benzene molecules. We discuss the feasibility of the cascading third-order process as a sensitive probe for the microscopic structures that are formed in liquids and solutions.

Journal Article↗
PubMed2001

Local structure analysis of Ti species stabilized in ion exchangeable layer solids by x-ray absorption spectroscopy.

Nano-sized titanium dioxides are incorporated into the interlayer spaces of ion-exchangeable layered perovskites, H(1-x)Ca2(x)La(x)Nb3O10 (x=0.0-0.75), by replacing the interlayer protons with positively charged TiO2 nano-sol particles or basic titanium glycolate complex (titanatrane). Powder X-ray diffraction analysis. UV-Vis absorption spectroscopy, thermogravimetric analysis, and N2 adsorption-desorption isotherm measurements show that quantum sized TiO2 particles are stabilized in between perovskite lattices to form micropores (S(BET) = 37-110 m2/g). X-ray absorption spectroscopy at the Ti K-edge was used for investigating the local environment around Ti atoms constituting the interlayer pillars. According to the XANES spectra, the 'as-pillared' Ti species have the same local environments with those of precursory species, which subsequently converted into TiO2 clusters with rutile and anatase-like local structures when TiO2 nano-sol particles and titanatrane are used as pillaring species. respectively. It is also found that the local environment of TiO2 remains almost constant irrespective of the layer charge density, while the TiO2 pillar content and the microporosity increase with the latter.

Journal Article↗
PubMed2001

Connecting local structure to interface formation: a molecular scale van der Waals theory of nonuniform liquids.

This article reviews a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. The method optimally combines two standard approximations, molecular (mean) field theory to describe interface formation and linear response (or Gaussian fluctuation) theory to describe local structure. Accurate results have been found in many different applications in nonuniform simple fluids and these ideas may have important implications for the theory of hydrophobic interactions in water.

Binding Sites↗
PubMed2003

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

This article presents an overview of the SAM-T02 method for protein fold recognition and the UNDERTAKER program for ab initio predictions. The SAM-T02 server is an automatic method that uses two-track hidden Markov models (HMMS) to find and align template proteins from PDB to the target protein. The two-track HMMs use an amino acid alphabet and one of several different local structure alphabets. The UNDERTAKER program is a new fragment-packing program that can use short or long fragments and alignments to create protein conformations. The HMMs and fold-recognition alignments from the SAM-T02 method were used to generate the fragment and alignment libraries used by UNDERTAKER. We present results on a few selected targets for which this combined method worked particularly well: T0129, T0181, T0135, T0130, and T0139.

Algorithms↗
PubMed2006

Characterization of the local structures of Ti-MCM-41 and their photocatalytic reactivity for the decomposition of NO into N2 and O2.

Ti-MCM-41 mesoporous molecular sieves were prepared at ambient temperature and were characterized by X-ray absorption near-edge structure and extended X-ray absorption fine structure, UV-vis, Fourier transform infrared spectroscopy, and photoluminescence spectroscopic analyses. It was found that an increase in the Ti content caused the structure of the Ti-oxides in Ti-MCM-41 to change from an isolated tetrahedral coordination to adjacent Ti-oxide species with Ti4+ of tetrahedral coordination. The photocatalytic reactivity of these catalysts for the decomposition of NO into N2 and O2 was found to strongly depend on the local structure of the Ti-oxide species including their coordination and distribution, i.e., the charge transfer excited state of the highly dispersed isolated tetrahedrally coordinated Ti-oxides act as the active sites for the photocatalytic decomposition of NO into N2 and O2.

Journal Article↗
PubMed1998

NMR study on the impact of metal ion binding and deoxynucleotide substitution upon local structure and stability of a small ribozyme.

We have studied a very small ribozyme described earlier which requires the presence of soft metal ions like manganese or cadmium. It consists of only three uridines as ribozyme, cleaving the sequence 5'-GAAA-3' after the guanosine. We have set out to characterize the metal ion binding in this system by NMR spectroscopy and the impact of the ribose 2'-OH group of the cleavable nucleotide upon local structure. NMR results indicate a high degree of regularity and order in the pyrimidine-rich ribozyme strand, and high flexibility within the purine-rich substrate. The guanosine 2'-hydroxy group adjacent to the cleavage site was found to have a profound effect upon the structure, apparently destabilizing a stacked arrangement. Metal ions were found to bind in a rather unspecific way, however, in the presence of higher amounts of divalent ions a preference in the vicinity of the cleavage site could be observed. 113Cd NMR spectra suggest a specific binding of Cd2+ ions to the RNA.

Adenosine↗
PubMed2001

The EXAFS study on the local structure of lanthanum in spinach PSII.

The complex of photosystem II (PSII) had been prepared from spinach by treatment with Triton X-100. The PSII, which had been depleted of the extrinsic 17- and 23-kDa polypeptides, was obtained by exposing the solution to a high concentration of NaCl, and the complex of PSII-La3+ was prepared by treatment with LaCl3. The result indicated that La3+ could inhibit the oxygen-evolution activity of PSII by replacing the Ca2+. The local structural environment of La in PSII has been also studied by using extended X-ray absorption fine structure (EXAFS). The primary result of EXAFS indicated that La coordinated with eight oxygen and/or nitrogen atoms, with the distance of the La-O/N bond being 2.5 A. In addition, La coordinated with four carbon atoms, with a distance of 3.5 A in the second shell. In the third shell, La coordinated with two manganese atoms, with the distance of La-Mn bond being 4.49 A, and it was also found that the La-Mn distance (4.49 A) was longer than that of Ca-Mn (3.3 A) (1) in PSII.

Calcium↗
PubMed2004

Relationship between local structural entropy and protein thermostability.

We developed a technique to compute structural entropy directly from protein sequences. We explored the possibility of using structural entropy to identify residues involved in thermal stabilization of various protein families. Examples include methanococcal adenylate kinase, Ribonuclease HI and holocytochrome c(551). Our results show that the positions of the largest structural entropy differences between wild type and mutant usually coincide with the residues relevant to thermostability. We also observed a good linear relationship between the average structural entropy and the melting temperatures for adenylate kinase and its chimeric constructs. To validate this linear relationship, we compiled a large dataset comprised of 1153 sequences and found that most protein families still display similar linear relationships. Our results suggest that the multitude of interactions involved in thermal stabilization may be generalized into the tendency of proteins to maintain local structural conservation. The linear relationship between structural entropy and protein thermostability should be useful in the study of protein thermal stabilization.

Adenylate Kinase↗
PubMed2000

Local structural elements in the mostly unstructured transcriptional activation domain of human p53.

DNA transcription is initiated by a small regulatory region of transactivators known as the transactivation domain. In contrast to the rapid progress made on the functional aspect of this promiscuous domain, its structural feature is still poorly characterized. Here, our multidimensional NMR study reveals that an unbound full-length p53 transactivation domain, although similar to the recently discovered group of loosely folded proteins in that it does not have tertiary structure, is nevertheless populated by an amphipathic helix and two nascent turns. The helix is formed by residues Thr(18)-Leu(26) (Thr-Phe-Ser-Asp-Leu-Trp-Lys-Leu-Leu), whereas the two turns are formed by residues Met(40)-Met(44) and Asp(48)-Trp(53), respectively. It is remarkable that these local secondary structures are selectively formed by functionally critical and positionally conserved hydrophobic residues present in several acidic transactivation domains. This observation suggests that such local structures are general features of acidic transactivation domains and may represent "specificity determinants" (Ptashne, M., and Gann, A. A. F. (1997), Nature 386, 569-577) that are important for transcriptional activity.

Amino Acid Sequence↗
PubMed2006

Investigations on the effect of Mn ions on the local structure and photocatalytic activity of Cu(I)-ZSM-5 catalysts.

The introduction of Mn ions into Cu(I)-ZSM-5 was found to lead to an enhancement of the photocatalytic activity for the direct decomposition of N2O into N2 and O2 at 298 K. Various in-situ techniques such as ESR, photoluminescence, XAFS as well as a combination of CO-FT-IR and CO-TPD measurements revealed that the accommodation of Mn ions within ZSM-5 zeolite cavities significantly affects the location sites of the ion-exchanged Cu(II) ions as well as the local structure of the Cu(I) ion species formed by evacuation at high temperatures. Moreover, the introduction of Mn ions into ZSM-5 led to an increase in the amount of 3-coordinated Cu(I) species at the main channel of the zeolite, playing a major role as the active species for the photocatalytic decomposition of N2O into N2 and O2.

Journal Article↗
PubMed1981

Fluorimetry study of N-(1-pyrenyl)iodoacetamide-labelled F-actin. Local structural change of actin protomer both on polymerization and on binding of heavy meromyosin.

A fluorescent reagent, N-(1-pyrenyl)iodoacetamide, was conjugated to rabbit skeletal muscle actin at the site of the most reactive sulfhydryl group, and fluorescence characteristics (excitation and emission spectra, quantum yields, lifetimes) of the conjugate were investigated. Associated with polymerization of labelled G-actin, the fluorescence intensity at 407 nm, after excitation at 365 nm, was enhanced by a factor of about 25. It was reduced to about 25% on the binding of heavy meromyosin (or subfragment 1). The results suggest that binding of heavy meromyosin to the protomer of F-actin alters the local structure of the protomer towards a G-actin-like one.

Actins↗
PubMed2003

Efficient remote homology detection using local structure.

MOTIVATION: The function of an unknown biological sequence can often be accurately inferred if we are able to map this unknown sequence to its corresponding homologous family. At present, discriminative methods such as SVM-Fisher and SVM-pairwise, which combine support vector machine (SVM) and sequence similarity, are recognized as the most accurate methods, with SVM-pairwise being the most accurate. However, these methods typically encode sequence information into their feature vectors and ignore the structure information. They are also computationally inefficient. Based on these observations, we present an alternative method for SVM-based protein classification. Our proposed method, SVM-I-sites, utilizes structure similarity for remote homology detection. RESULT: We run experiments on the Structural Classification of Proteins 1.53 data set. The results show that SVM-I-sites is more efficient than SVM-pairwise. Further, we find that SVM-I-sites outperforms sequence-based methods such as PSI-BLAST, SAM, and SVM-Fisher while achieving a comparable performance with SVM-pairwise. AVAILABILITY: I-sites server is accessible through the web at http://www.bioinfo.rpi.edu. Programs are available upon request for academics. Licensing agreements are available for commercial interests. The framework of encoding local structure into feature vector is available upon request.

Algorithms↗
PubMed2001

High-resolution X-ray spectroscopy of rare events: a different look at local structure and chemistry.

The combination of large-acceptance high-resolution X-ray optics with bright synchrotron sources permits quantitative analysis of rare events such as X-ray fluorescence from very dilute systems, weak fluorescence transitions or X-ray Raman scattering. Transition-metal Kbeta fluorescence contains information about spin and oxidation state; examples of the characterization of the Mn oxidation states in the oxygen-evolving complex of photosystem II and Mn-consuming spores from the marine bacillus SG- are presented. Weaker features of the Kbeta spectrum resulting from valence-level and 'interatomic' ligand to metal transitions contain detailed information on the ligand- atom type, distance and orientation. Applications of this spectral region to characterize the local structure of model compounds are presented. X-ray Raman scattering (XRS) is an extremely rare event, but also represents a unique technique to obtain bulk-sensitive low-energy (<600 eV) X-ray absorption fine structure (XAFS) spectra using hard (approximately 10 keV) X-rays. A photon is inelastically scattered, losing part of its energy to promote an electron into an unoccupied level. In many cases, the cross section is proportional to that of the corresponding absorption process yielding the same X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) features. XRS finds application for systems that defy XAFS analysis at low energies, e.g. liquids or highly concentrated complex systems, reactive compounds and samples under extreme conditions (pressure, temperature). Recent results are discussed.

Bacillus↗
PubMed2006

E230Q mutation of the catalytic subunit of cAMP-dependent protein kinase affects local structure and the binding of peptide inhibitor.

The active site of the mammalian cAMP-dependent protein kinase catalytic subunit (C-subunit) has a cluster of nonconserved acidic residues-Glu127, Glu170, Glu203, Glu230, and Asp241-that are crucial for substrate recognition and binding. Studies have shown that the Glu230 to Gln mutant (E230Q) of the enzyme has physical properties similar to the wild-type enzyme and has decreased affinity for a short peptide substrate, Kemptide. However, recent experiments intended to crystallize ternary complex of the E230Q mutant with MgATP and protein kinase inhibitor (PKI) could only obtain crystals of the apo-enzyme of E230Q mutant. To deduce the possible mechanism that prevented ternary complex formation, we used the relaxed-complex method (Lin, J.-H., et al. J Am Chem Soc 2002, 24, 5632-5633) to study PKI binding to the E230Q mutant C-subunit. In the E230Q mutant, we observed local structural changes of the peptide binding site that correlated closely to the reduced PKI affinity. The structural changes occurred in the F-to-G helix loop and appeared to hinder PKI binding. Reduced electrostatic potential repulsion among Asp241 from the helix loop section and the other acidic residues in the peptide binding site appear to be responsible for the structural change.

Binding Sites↗
PubMed2001

Deletion of specific glycan chains affects differentially the stability, local structures, and activity of lecithin-cholesterol acyltransferase.

The enzymatic and interfacial binding activity of lecithin-cholesterol acyltransferase (LCAT) is affected differentially by the location and extent of its glycosylation. Two LCAT glycosylation-deficient mutants, N84Q and N384Q, were constructed, permanently expressed in Chinese hamster ovary cells, and purified to determine the effects of deleting individual glycan chains on its stability, structure, and function. These purified mutants were studied by spectroscopic structural methods and enzymatic and binding assays to develop a molecular rationale for the relationship between LCAT glycosylation and activity. The N84Q LCAT mutant did not possess measurable enzymatic activity or interfacial binding affinity for reconstituted high-density lipoproteins. In addition, in thermal and chemical denaturation studies, N84Q LCAT was found to be significantly less stable than wild-type LCAT. The N384Q variant was initially more enzymatically active than wild-type LCAT, but gradually lost activity within months; however, it retained full interfacial binding activity. Significant changes were detected over time by circular dichroism in the alpha-helical content of N384Q LCAT and in the beta-sheet content of N84Q LCAT, compared with wild-type LCAT. Fluorescence measurements with the probe 1-anilinonapthalene-8-sulfonate suggested an alteration of the active site cavity in both mutants. In conclusion, both mutants lost catalytic activity, N84Q shortly after purification and N384Q more gradually, and were destabilized, probably because the deletion of the glycan chains altered local structural elements near the active site cavity and/or the interfacial binding regions.

Amino Acid Sequence↗
PubMed2006

Local structure of actinide dioxide solid solutions Th(1-x)U(x)O2 and Th(1-x)Pu(x)O2.

Extended X-ray absorption fine structure (EXAFS) has been utilized to investigate the local atomic structure around Th, U, and Pu atoms in polycrystalline mixed dioxides Th(1-x)M(x)O2 (with M = U, Pu) for x ranging from 0 to 1. The composition dependence of the two first-coordination-shell distances was measured throughout the entire composition range for both solid solutions. The first-shell distances vary slightly across the solid-solution composition with values close to those of the pure dioxide parents, indicating a bimodal cation-oxygen distribution. In contrast, the second-shell distance varies strongly with composition, with values close to the weighted amount average distances. Nevertheless, in both systems, the lattice cell parameters, deduced from the first- and second-shell bond determined by EXAFS, are very close to those measured from X-ray diffraction (XRD). They vary linearly with composition, accurately following Vegard's law.

Journal Article↗