Local Structural Deformation Research Articles

Ligand-induced global transitions in the catalytic domain of protein kinase A

Conformational transitions play a central role in the phosphorylation mechanisms of protein kinase. To understand the nature of these transitions, we investigated the dynamics of nucleotide binding to the catalytic domain of PKA, a prototype for the protein kinase enzyme family. The open-to-closed transition in PKA was constructed as a function of ATP association by using available X-ray data and Brownian dynamics. Analyzing the multiple kinetic trajectories at the residue level, we find that the spatial rearrangement of the residues around the nucleotide-binding pocket, along with suppressed local fluctuations, controls the compaction of the entire molecule. In addition, to accommodate the stresses induced by ATP binding at the early transition stage, partial unfoldings (cracking) and reformations of several native contacts occur at the interfaces between the secondary structure motifs enveloping the binding pocket. This suggests that the enzyme experiences local structural deformations while reaching its functional, ATP-bound state. Our dynamical view of the ligand-induced transitions in PKA suggests that the kinetic hierarchy of local and global dynamics, the variable fluctuation of residues and the necessity of partial local unfolding may be fundamental components in other large scale allosteric transitions.

The directional emission sensitivity of photonic crystal waveguides to air hole removal

To obtain highly directional light output from photonic crystal waveguides (PCWs), the emission characteristics of the narrow-width waveguide structures are investigated by tailoring the geometry of the exit sides. The local structural deformations in the form of air hole removal from the triangular-lattice photonic crystal (PC) show the effectiveness of the previously proposed approach that was implemented by us for another type of PC. The spatial broadening of the beam is greatly suppressed. With the modified waveguide exits, highly directional emissions with small side lobes are achieved. The frequency dependency of the directional emissions is evaluated. We show that the divergence angles of the beams depend linearly on the wavelength for a regular type of PCW but the modified PCW exits have local minima with respect to wavelength in terms of the divergence angle. The present work may prove to be helpful in the design of couplers and edge-emitting lasers and in the implementation of free-space optical communications.

Interaction of Fullerol C60(OH)20 with Nucleic Acids

Functionalized fullerenes have received much attention during the recent decade in view of their potential use in in vivo imaging, drug transport, and even functioning as the drugs themselves as HIV-1 protease inhibitors, antioxidants, and neuroprotective agents [1]. Yet, the use of functionalized nanoparticles in such applications is shadowed by the lack of reliable information on their fundamental interaction mechanisms with biological systems. This entails not only specific atomistic interaction mechanisms between individual molecules but also transformation and non-covalent functionalization of the nanoparticles used within a biological organism. For interactions between nanoparticles and RNA or DNA, interference with their regular functioning or induction of damage by, e.g. photocleavage, may offer new routes for biomedical engineering - but potentially also for a number of unwanted effects in cells and bacteria.We have used atomistic molecular dynamics simulations to study the interaction of polyhydroxylated fullerenes C60(OH)20, i.e. fullerols, with nucleic acids ssRNA, ssDNA and dsDNA. The nucleic acids are modeled by oligomers of 20 arbitrary nucleotide (bp) sequences. The modeling provides atomic-scale information on the binding modes of the fullerols, as well as local structural deformation of nucleic acids by the fullerol binding. The data obtained from the simulations is compared to spectroscopic measurements on solutions containing such nucleic acids and fullerols.[1] T. Da Ros and M. Prato, Chem. Commun., 1999, 663-669.

Effect of the Si/Zr molar ratio on the synthesis of Zr-based mesoporous molecular sieves

Highly ordered Zr-based mesoporous molecular sieves were synthesized via a surfactant-templated method and the effect of the Si/Zr molar ratio on the crystalline structure, textural properties and surface acidity were studied by XRD, FTIR, TEM and 29Si MAS-NMR techniques. FTIR spectra show that the intensity of the band around 890 cm −1 which corresponds to the vibration of Si–O–Zr bond was increased with increasing of the zirconium content, therefore, this band may be used as an indicator of the degree of the zirconium incorporation into the Si-framework. When the zirconium content increased in the materials, the Q 3/ Q 4 value obtained from 29Si MAS-NMR was linearly increased, whereas, the intensity the XRD peaks was gradually reduced; as a result, the pore wall thickness of the resultant materials was gradually increased, the surface area and the structural regularity were diminished. In order to obtain Zr-MCM-41 with highly ordered mesostructure and large surface area, proper Si/Zr molar ratio is a key factor, e.g., Si/Zr should be no less than 10. It was also found that the Brønsted acid sites which resulted from charge unbalance or local structure deformation due to the Zr 4+ incorporation into the vicinity of the hydroxyls carrying silicon were created on the surface of the Zr-MCM-41 solids; strong Brønsted acidity could be formed on the solid with high zirconium content.

TRLFS characterization of Eu(III)-doped synthetic organo-hectorite

Europium(III) was coprecipitated with the clay mineral hectorite, a magnesian smectite, following a multi-step synthesis procedure. Different Eu(III) species associated with the proceeding synthetic hectorite were characterized by selectively exciting the 5D 0→ 7F 0 transition at low temperature (T < 20 K). Fluorescence decay times indicated that Eu(III) ions may be incorporated in the octahedral layer of the brucite precursor as well as in the octahedral sheet of the clay mineral. The excitation spectra indicated that the substitution of the divalent Mg by the trivalent Eu induced local structural deformation. This investigation implements the molecular-level understanding of the f element structural incorporation into the octahedral layer of sheet silicates by coprecipitation with clay minerals from salt solutions at 100 °C.

Magnetism in germanium-doped boron-nitride nanotubes

Abstract The magnetic property of the pristine and germanium-doped (10, 0) boron-nitride (BN) nanotube has been studied using a DFT-LSDA method. The germanium substitution for either a single boron or single nitrogen atom yields a spin-polarized, almost dispersionless π bands within the original band gap and net magnetic moment is 1 μ B . The flat band originates from the local structural deformation in the vicinity of germanium atom. Contrast to the theoretical models based on carbon or silicon-doped BN nanotubes, substituting a nitrogen atom with germanium atom results in three pairs of in-gap states which indicates more extended nanotube deformation than those previously studied.

Ferroic clustering and phonon anomalies in Pb-based perovskite-type relaxors

The phonon anomalies and their relationship to the structural inhomogeneitiesin Pb-based relaxors are studied on the basis of stoichiometricPbSc0.5Ta0.5O3 andPbSc0.5Nb0.5O3 and Nb-, Sn- andBa-containing PbSc0.5Ta0.5O3. The ferroic clustering and the development of the ferroelectric state canbe followed by analysing quantitatively the intensity ratios of the Ramanscattering arising from the corresponding local structural distortions.PbSc0.5Ta0.5O3 and PbSc0.5Nb0.5O3 differ from each other in the length of coherence of Pb shifts from the O layers,which leads to dissimilarities in the ferroelectric state. The incorporation ofadditional elements in the cation positions heavily influences the incipientferroic species and restrains the formation of proper ferroelectric state, thusfavouring the non-ergodic state. The partial substitution of Ba for Pb andSn4+ for the B-type cations induces additional local structural deformations consisting mainly ofBO6 distortion along the three-fold and four-fold octahedral axes of symmetry, respectively.

Ion channels of glutamate receptors: structural modeling

Ionotropic glutamate receptors belong to the superfamily of P-loop channels as well as K(+), Na(+), and Ca(2+) channels. However, the structural similarity between ion channels of the glutamate receptors and K(+) channels is a matter of discussion. The aim of this study was to analyze differences between the structures of K(+) channels and glutamate receptor channels. For this purpose, homology models of NMDA and AMPA receptor channels (M2 and M3 segments) were built using X-ray structures of K(+) channels as templates. The models were optimized and used to reproduce specific data on the structure of glutamate receptor channels. Particular attention was paid to the data of the binding of channel blockers and to the results of scanning mutagenesis. The modeling demonstrates that properties of glutamate receptor channel can be reproduced assuming only local structural deformations of the K(+) channel templates. The most valuable differences were found in the selectivity-filter region, whereas helical parts of M2 and M3 segments could have similar spatial organization with homologous segments in K(+) channels. It is concluded that the current experimental data on glutamate receptor channels does not reveal global structural differences with K(+) channels.

The influence of the interfacial FeMn insertion layer on the pinning effect of IrMn/CoFe exchange coupled bilayers

The exchange bias and thermal stability of CoFe/IrMn films with and without thin FeMn layer at the interface were investigated. Very thin FeMn insertion layer was found to increase the pinning field largely. An optimum pinning field of ∼220 Oe was obtained for the film CoFe (100 Å)/FeMn (1.5 Å)/IrMn (70 Å), while only 140 Oe was obtained for the film CoFe (100 Å)/IrMn (70 Å). Their coercivities were not much different. The two films’ pinning field dependences of temperature were also almost the same and their blocking temperatures were both about 250 °C. This is ascribed that the local structure deformations at the interface of CoFe/IrMn increase the net spins of the interfacial antiferromagnetic atoms, and hence the exchange bias strength.

28th DeBeers Alex. Du Toit Memorial Lecture, 2004. On Cryogenian (Neoproterozoic) ice-sheet dynamics and the limitations of the glacial sedimentary record

28th DeBeers Alex. Du Toit Memorial Lecture, 2004. On Cryogenian (Neoproterozoic) ice-sheet dynamics and the limitations of the glacial sedimentary record

Global Dynamics of Shaft Lines Rotating in Surrounding Fluids Application to Thin Fluid Films

While often sufficiently accurate, approaches using rotor dynamics and bladed disc dynamics are not adapted to the study of certain important cases, i.e., when observing wheel/shaft coupling or when fluid elements are strongly coupled with local structural deformations. The approach proposed here is a step toward a global model of shaft lines. The whole flexible wheel/shaft assembly and the influence of specific fluid film elements are considered in a full threedimensional model. A modal projection associated with a grid located at the interface of the fluid and structural domains provides an efficient and adaptable coupling. The equations governing the whole system are solved within a time marching procedure which alternatively considers the equations of fluid and structure. The technique chosen is applied to two different test cases. The first is composed of a disc and a thin‐walled shaft mounted on a hydrodynamic bearing. The second is intended for studying a more realistic structure composed of a shaft and a wheel coupled with a fluid film between the wheel and a casing. These applications make it possible to identify trends related to fluid effects and couplings between the flexible structural parts.

Infrared Study of Spin Crossover Fe–Picolylamine Complex

Infrared (IR) absorption spectroscopy has been used to probe the evolution of microscopic vibrational states upon the temperature- and photo-induced spin crossovers in [Fe(2-picolylamine)3]Cl2EtOH (Fe-pic). To overcome the small sizes and the strong IR absorption of the crystal samples used, an IR synchrotron radiation source and an IR microscope have been used. The obtained IR spectra of Fe-pic show large changes between high-spin and low-spin states for both the temperature- and the photo- induced spin crossovers. Although the spectra in the temperature- and photo-induced high-spin states are relatively similar to each other, they show distinct differences below 750 cm-1. This demonstrates that the photo-induced high-spin state involves microscopically different characters from those of the temperature-induced high-spin state. The results are discussed in terms of local pressure and structural deformations within the picolylamine ligands, and in terms of their possible relevance to the development of macroscopic photo-induced phase in Fe-pic.

Effects of Wheel-Shaft-Fluid Coupling and Local Wheel Deformations on the Global Behavior of Shaft Lines

Rotating parts of turbomachines are generally studied using different uncoupled approaches. For example, the dynamic behavior of shafts and wheels are considered independently and the influence of the surrounding fluid is often taken into account in an approximate way. These approaches, while often sufficiently accurate, are questionable when wheel-shaft coupling is observed or when fluid elements are strongly coupled with local structural deformations (leakage flow between wheel and casing, fluid bearings mounted on a thin-walled shaft, etc.). The approach proposed is a step toward a global model of shaft lines. The whole flexible wheel-shaft assembly and the influence of specific fluid film elements are considered in a fully three-dimensional model. In this paper, the proposed model is first presented and then applied to a simple disk-shaft assembly coupled with a fluid film clustered between the disk and a rigid casing. The finite element method is used together with a modal reduction for the structural analysis. As thin fluid films are considered, the Reynolds equation is solved using finite differences in order to obtain the pressure field. Data are transferred between structural and fluid meshes using a general method based on an interfacing grid concept. The equations governing the whole system are solved within a time-marching procedure. The results obtained show significant influence of specific three-dimensional features such as disk-shaft coupling and local disk deformations on global behavior.

Discordant paleomagnetic direction in Miocene rocks from the central Tarim Basin: evidence for local deformation and inclination shallowing

From exposures at the southeastern end of the Maza Tagh range in the central Tarim Basin (latitude: 38.5°N; longitude: 80.5°E), 55 paleomagnetic sites were collected from red mudstones and sandstones of the Miocene Wuqia Formation. Thermal demagnetization revealed a high unblocking temperature characteristic remanent magnetization (ChRM). Five sites collected across a kink fold yield a positive fold test at 99% confidence level. The mean directions computed from normal and reversed polarity sites are antipodal suggesting a primary origin for the ChRM. In stratigraphic coordinates, the final set of 30 site-mean ChRM directions yields a section-mean direction: inclination (I)=29.4°; declination (D)=24.7°; α95=6.2°. When compared to the Miocene expected direction (at 20 Ma), the observed direction indicates 30.8±5.5° flattening of inclination and 15.3±6.7° clockwise vertical-axis rotation. Anisotropy of magnetic susceptibility measurements on 155 samples show a strong foliation of 1.092 with a sub-vertical minimum susceptibility axis. These observations indicate a rock-magnetic (depositional or compaction shallowed) origin for the inclination flattening. The clockwise deflection of the observed declination can be interpreted as either: (1) 15.3±6.7° clockwise rotation of the entire Tarim Basin since the Miocene; or (2) a local km-scale structural deformation. It is not a simple matter to discard the interpretation of 15.3±6.7° clockwise rotation of the Tarim Basin because the fastest rates of rotation determined from global positioning system and slip-rate studies of Quaternary faults could produce such a rotation if extrapolated to 20 Ma. Nevertheless, we argue that local deformation is the preferred interpretation because the map pattern of local structures shows ∼20° clockwise deflection toward the southeastern end of the Maza Tagh range where the paleomagnetic samples were collected.

Coupling of Small Lattice Polarons to Magnetic Field in Magnetoresistive Manganites

We report Extended X-Ray Absorption Fine Structure measurements at the Mn K absorption edge on hole doped manganese oxides ${La}_{1-x}Ca_x{MnO}_3$ in a wide temperature range above and below the metal insulator transition temperature in presence of a magnetic field. In accordance with previous studies an anomalous increase in the Debye Waller factors is detected at the phase transition in the first coordination shell made up of O atoms. This is due to a local structural deformation around $Mn^{3+}$ atoms associated with the Jahn-Teller effect and the formation of polarons. The application of a magnetic field results in a variation of this deformation with a thermal behaviour that closely resembles that of the magnetoresistance. This confirms the relevance of the polarons on the conductivity properties of such materials. The magnetic field has a huge effect on the second coordination shell probably related with the change of the Mn-O-Mn angle upon application of the magnetic field.

Salt Effects on Fluorescence Spectral Shifts of DNA-Bound Hoechst 33258 and Reaction Volumes of the Minor Groove Binding

Abstract In this study, salt effects on the interaction of Hoechst 33258 (2′-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5′-bi-1H-benzimidazole trihydrochloride) with several synthetic polynucleotide duplexes were studied by fluorescence spectral shifts and reaction volumes derived from the pressure dependence of binding equilibria. Both the excitation and emission spectra of Hoechst 33258 saturated by polyd(A)·polyd(T) or poly[d(A-T)]·poly[d(A-T)] shifted to shorter wavelengths as NaCl concentrations increased. The peak intensities first increased ([NaCl] &amp;lt; 100 mM) then started to decrease ( &amp;gt; 100 mM NaCl). Salt dependent blue shifts were also observed in their absorption spectra. These results were in contrast to what occurred to the drug complexed with poly[d(G-C)]·poly[d(G-C)] or poly[d(A-G)]·poly[d(C-T)]. The pressure dependence of the association equilibrium constants (Kp) of the drug and two A·T polymers was examined at several salt concentrations; the results helped to derive reaction volumes. In the case of the A-T copolymer, negative volume changes were found at all ionic concentrations studied. In contrast, in the case of the homopolymer, negative volume changes were found at lower salt concentrations (10 and 50 mM) while positive ones were found at higher concentrations (100 and 200 mM NaCl). These results are discussed in terms of the local structural deformation and hydration rearrangement of DNA.

X-ray diffraction study of[Zn(1−propyltetrazole)6](BF4)2single crystal

Single-crystal structure determination of ${[\mathrm{Zn}(\mathrm{ptz})}_{6}{](\mathrm{B}\mathrm{F}}_{4}{)}_{2}$ has been performed at 110 and 190 K in order to investigate the possible existence of a local structural deformation proposed by positron annihilation study of Nagai et al. [Phys. Rev. B 57, 14 119 (1998)]. A large thermal contraction along the $c$ axis with decreasing temperature is observed, while the displacement of the atoms within the $\mathrm{ab}$ plane is very small. This implies that the effect observed in the positron annihilation spectroscopies is caused by interactions involving positronium.

On the multiple peak structure of electronic Raman scattering spectra in Ce-doped Nd 2CuO 4

The origin of the multiple peak structure of the electronic Raman scattering spectra in Ce-doped Nd 2CuO 4 is examined using the superposition model of the crystal field. Results of the model calculation based on available local structure data indicate that the Raman structure examined arises due to the Ce-doping induced local structure deformation associated with charge transfer.

The effect of the temperature of Na-Y zeolite treatment with ethylenediaminetetraacetic acid on its structure

The variations in the structure of Na-Y zeolite after its dealumination with ethylenediaminetetraacetic acid at 293 and 373 K were studied by IR spectra of lattice vibrations. The resulting deformation of the terminal [O3SiO](H,Na) tetrahedra is accompanied by the closure of the terminal ≡Si-O(H,Na) groups with the formation of bridge bonds. The saturation of samples dealuminated at 373 K with water decreases the deformation of the terminal tetrahedra which recovers on heating. Long-term exposure to water vapor results in an irreversible decrease in local deformations and in lowering the excessive negative charge of the skeleton, which manifests itself in a general high-frequency shift of the bands by 5–7 cm−1. These changes are more pronounced when the samples are heated in air at 873 K. The local structure deformations of the samples dealuminated at 293 K are irreversible. Heating them at 873 K causes the reorganization of the structure with the formation of a silica phase.

Three-dimensional structure of proteinase K at 0.15-nm resolution.

The crystal and molecular structure of proteinase K was determined by X-ray diffraction data to 0.15-nm resolution. The enzyme belongs to the subtilisin family with an active-site catalytic triad Asp39--His69--Ser224 but is a representative of a subgroup with a free Cys73 close to and 'below' the active His69. Besides this Cys72, proteinase K has two disulfide bonds, Cys34--Cys123 and Cys178--Cys249, which contribute to the stability of the tertiary structure consisting of an extended central parallel beta-sheet decorated by six alpha-helices, three short antiparallel beta-sheets, 18 beta-turns and involving several internal, structurally important water molecules. Proteinase K exhibits two Ca2+-binding sites, one very strong and the other weak, which were the sites of the heavy atoms (Pb2+, Sm3+) used to solve the crystal structure. The weak binding site is liganded to the N and C termini, Thr16 and Asp260, and is only incompletely coordinated by oxygen ligands. The strong binding site is coordinated in the form of a pentagonal bipyramid with the side chain carboxylate of Asp200 and the C = O of Pro175 as apex, and C = O of Val177 and four water molecules in the equatorial plane. Upon removal of this Ca2+, proteinase K loses activity which is interpreted in terms of a local structural deformation involving the substrate-recognition site (Ser132--Gly136), probably associated with a cis----trans isomerization of cis Pro171. Several water molecules are located in the active site. One, W335, is positioned in the 'oxyanion hole' and is displaced by the C = O of the scissile peptide bond of the substrate, as indicated by crystallographic studies with peptide chloromethane inhibitors. Based on these experiments, a reaction mechanism is proposed where the peptide substrate forms a three-stranded antiparallel pleated sheet with the recognition site of proteinase K consisting of Ser132--Leu133--Gly134 on one side and Gly100--Ser101 on the other, followed by expulsion of the oxyanion hole water W335 and hydrolytic cleavage by the Asp39--His69--Serr224 triad. These latter residues display low thermal motion corresponding to well-defined geometry and are hardly accessible to solvent molecules, whereas the recognition-site amino acids are more flexible and partially exposed to solvent.