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Structural Transition (structural + transition)
Selected AbstractsUniversal Behavior and Electric-Field-Induced Structural Transition in Rare-Earth-Substituted BiFeO3ADVANCED FUNCTIONAL MATERIALS, Issue 7 2010Daisuke Kan Abstract The discovery of a universal behavior in rare-earth (RE)-substituted perovskite BiFeO3 is reported. The structural transition from the ferroelectric rhombohedral phase to an orthorhombic phase exhibiting a double-polarization hysteresis loop and substantially enhanced electromechanical properties is found to occur independent of the RE dopant species. The structural transition can be universally achieved by controlling the average ionic radius of the A-site cation. Using calculations based on first principles, the energy landscape of BiFeO3 is explored, and it is proposed that the origin of the double hysteresis loop and the concomitant enhancement in the piezoelectric coefficient is an electric-field-induced transformation from a paraelectric orthorhombic phase to the polar rhombohedral phase. [source] Using Pressure to Provoke the Structural Transition of Metal,Organic Frameworks,ANGEWANDTE CHEMIE, Issue 41 2010Dr. Isabelle Beurroies Poröse Festkörper unter Druck: Eine Hysterese des Ein- und Ausströmens von Quecksilber in MIL-53(Cr)-Partikel wird mit einem Übergang von groß- zu kleinporigen Formen des Metall-organischen Gerüstmaterials erklärt, der aus dem isostatischen Druck des Quecksilbermediums um die porösen Partikel folgt. Das beobachtete Verhalten, das qualitativ durch ein einfaches energetisches Modell wiedergegeben wird, deutet auf Anwendungsmöglichkeiten als molekulare Stoßdämpfer oder Schraubenfeder hin. [source] Effect of Putrescine and PEG on a Structural Transition of DNA G-QuadruplexCHEMINFORM, Issue 9 2004Daisuke Miyoshi Abstract For Abstract see ChemInform Abstract in Full Text. [source] Redox Activity and Structural Transition of Heptyl Viologen Adlayers on Cu(100),CHEMPHYSCHEM, Issue 7 2010Min Jiang Dr. Abstract The redox behaviour and potential-dependent adsorption structure of heptyl viologen (1,1,-diheptyl-4,4,-bipyridinium dichloride, DHV2+) on a Cu(100) electrode was investigated in a chloride-containing electrolyte solution by cyclic voltammetry (CV) and in situ electrochemical scanning tunneling microscopy (EC,STM). The dicationic DHV molecules generate a few pairs of current waves in CV measurements which are ascribed to two typical one-electron transfer steps. STM images obtained in a KCl-containing electrolyte solution disclose a well-ordered c(2×2) chloride adlayer on a Cu(100) electrode surface. After injecting DHV2+ molecules into the KCl electrolyte solution, a highly ordered 2D "dot-array" structure in STM images emerges on the c(2×2)-Cl modified Cu(100) electrode surface. DHV2+ molecules spontaneously arrange themselves with their molecular planes facing the electrode surface and their long molecular axis parallel to the step edge. Such adsorption structure can be described by mirror domains and rotational domains which stably exist between 200 mV and ,100 mV. One-electron reduction of the dications DHV2+ around ,150 mV causes a phase transition from a ,dot-array' assembly to a stripe pattern formed by DHV.+ radical monocations in STM images which has a bilayer structure. With a further decrease of the applied electrode potential, the structure of the DHV.+ adlayer undergoes a change from a loose stripe phase to a more compact stripe phase, a subsequent decay of the compact structure, and finally the formation of a new dimer phase. A further electron transfer reaction at ,400 mV causes the formation of an amorphous phase on the chloride free electrode surface. In a reverse anodic sweep, the reproduction of the ordered DHV.+ stacking phase occurs again on top of the chloride lattice. [source] Structural transition during thermal denaturation of collagen in the solution and film states,CHIRALITY, Issue 1 2009Ganesh Shanmugam Abstract Temperature dependent vibrational circular dichroism (VCD) spectra of type I collagen, in solution and film states, have been measured. These spectra obtained for solution sample suggest that the thermal denaturation of collagen results in transition from poly- L -proline II (PPII) to unordered structure. The PPII structure of collagen is identified by the presence of negative VCD couplet in the amide I region, while the formation of unordered structure is indicated by the disappearance of VCD in the amide I region. The temperature dependent spectra obtained for the supported collagen film indicated a biphasic transition, which is believed to be the first vibrational spectroscopic report to support a biphasic transition during thermal denaturation of collagen film. The temperature dependent spectra of collagen films suggest that the thermal stability of collagen structure depends on its state and decreases in the order: supported film > free standing film > solution state. These observations are believed to be significant in the VCD spectroscopic analysis of secondary structures of proteins and peptides. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] Structural transitions in solidsACTA CRYSTALLOGRAPHICA SECTION A, Issue 5 2010Stefano Leoni First page of article [source] An Individual Carbon Nanotube Transistor Tuned by High PressureADVANCED FUNCTIONAL MATERIALS, Issue 19 2010Christophe Caillier Abstract A transistor based on an individual multiwalled carbon nanotube is studied under high-pressure up to 1 GPa. Dramatic effects are observed, such as the lowering of the Schottky barrier at the gold,nanotube contacts, the enhancement of the intertube conductance, including a discontinuity related to a structural transition, and the decrease of the gate hysteresis of the device. [source] Structural disorder in amyloid fibrils: its implication in dynamic interactions of proteinsFEBS JOURNAL, Issue 19 2009P. Tompa Proteins are occasionally converted from their normal soluble state to highly ordered fibrillar aggregates (amyloids), which give rise to pathological conditions that range from neurodegenerative disorders to systemic amyloidoses. Recent methodological advances in solid-state NMR and EPR spectroscopy have enabled determination of the 3D structure of several amyloids at residue-level resolution. The general picture that emerges is that amyloids constitute parallel , sheets, in which individual polypeptide chains run roughly perpendicular to the major axis of the fibril and are stacked in-register. Thus, the unifying theme of amyloid formation is the structural transition from an initial globular or intrinsically disordered state to a highly ordered regular form. In this minireview, we show that this description is somewhat oversimplified, because part of the polypeptide chain in the amyloid remains intrinsically disordered and does not become part of the ordered core. As demonstrated through examples such as the amyloids of ,-synuclein and A, peptide and the yeast prions HET-s and Ure2p, these disordered segments are depleted in amino acids NQFYV and are enriched in DEKP. They are also significantly more charged and have a higher predicted disordered value than segments in the cross-, core. We suggest that structural disorder in amyloid is a special case of ,fuzziness', i.e. disorder in the bound state that may serve different functions, such as the accommodation of destabilizing residues and the mediation of secondary interactions between protofibrils. [source] Characterization of carbonic anhydrase from Neisseria gonorrhoeaeFEBS JOURNAL, Issue 6 2001Björn Elleby We have investigated the steady state and equilibrium kinetic properties of carbonic anhydrase from Neisseria gonorrhoeae (NGCA). Qualitatively, the enzyme shows the same kinetic behaviour as the well studied human carbonic anhydrase II (HCA II). This is reflected in the similar pH dependencies of the kinetic parameters for CO2 hydration and the similar behaviour of the kinetics of 18O exchange between CO2 and water at chemical equilibrium. The pH profile of the turnover number, kcat, can be described as a titration curve with an exceptionally high maximal value of 1.7 × 106 s,1 at alkaline pH and a pKa of 7.2. At pH 9, kcat is buffer dependent in a saturable manner, suggesting a ping-pong mechanism with buffer as the second substrate. The ratio kcat/Km is dependent on two ionizations with pKa values of 6.4 and 8.2. However, an 18O-exchange assay identified only one ionizable group in the pH profile of kcat/Km with an apparent pKa of 6.5. The results of a kinetic analysis of a His66,Ala variant of the bacterial enzyme suggest that His66 in NGCA has the same function as a proton shuttle as His64 in HCA II. The kinetic defect in the mutant can partially be overcome by certain buffers, such as imidazole and 1,2-dimethylimidazole. The bacterial enzyme shows similar Ki values for the inhibitors NCO,, SCN, and N3, as HCA II, while CN, and the sulfonamide ethoxzolamide are considerably weaker inhibitors of the bacterial enzyme than of HCA II. The absorption spectra of the adducts of Co(II)-substituted NGCA with acetazolamide, NCO,, SCN,, CN, and N3, resemble the corresponding spectra obtained with human Co(II)-isozymes I and II. Measurements of guanidine hydrochloride (GdnHCl)-induced denaturation reveal a sensitivity of the CO2 hydration activity to the reducing agent tris(2-carboxyethyl)phosphine (TCEP). However, the A292/A260 ratio was not affected by the presence of TCEP, and a structural transition at 2.8,2.9 m GdnHCl was observed. [source] Transition metal,boron complexes BnM: From bowls (n = 8,14) to tires (n = 14)JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2006Si-Dian Li Abstract Transition metal,boron complexes BnM have been predicted at density functional theory level to be molecular bowls (n = 8,14) hosting a transition metal atom (M) inside or molecular tires (n = 14) centered with a transition metal atom. Small Bn clusters prove to be effective inorganic ligands to all the VB,VIIIB transition metal elements in the periodic table. Density functional evidences obtained in this work strongly suggest that bowl-shaped fullerene analogues of Bn units exist in small BnM complexes and the bowl-to-tire structural transition occur to the first-row transition metal complexes BnM (M = Mn, Fe, Co) at n = 14, a size obviously smaller than n = 20 where the 2D-3D structural transition occurs to bare Bn. The half-sandwich-type B12Cr (C3v), full sandwich-type (B12)2Cr (D3d), bowl-shaped B14Fe (C2), and tire-shaped B14Fe (D7d) and B14Fe, (C7v) are the most interesting prototypes to be targeted in future experiments. These BnM complexes may serve as building blocks to form extended boron-rich BnMm tubes or cages (m , 2) or as structural units to be placed inside carbon nanotubes with suitable diameters. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] The global recession of 2009 in a long-term development perspectiveJOURNAL OF INTERNATIONAL DEVELOPMENT, Issue 6 2010Charles Gore Abstract This paper argues that the global recession of 2009 marks the ending of a global development cycle which began in the early 1950s. The long-wave rhythm of production and prices in the global development cycle is generated by the life cycle of investment and innovation during a technological revolution, related changes in supply and demand for natural resources, and inertia and transformation in the socio-institutional framework within which development takes place. From this perspective, the global recession is interpreted as a blocked structural transition. Whilst failings in the financial system triggered the global financial crisis, that crisis and the recession are more deeply rooted in contradictions in the global development trajectory. A paradigm shift in development theory and practice is a crucial element of the socio-institutional transformation now necessary to re-boot the global development cycle. Copyright © 2010 John Wiley & Sons, Ltd. [source] Effect of Interface Structure on the Microstructural Evolution of CeramicsJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 8 2006Wook Jo The interface atomic structure was proposed to have a critical effect on microstructure evolution during sintering of ceramic materials. In liquid-phase sintering, spherical grains show normal grain growth behavior without exception, while angular grains often grow abnormally. The coarsening process of spherical grains with a disordered or rough interface atomic structure is diffusion-controlled, because there is little energy barrier for atomic attachments. On the other hand, kink-generating sources such as screw dislocations or two-dimensional (2-D) nuclei are required for angular grains having an ordered or singular interface structure. Coarsening of angular grains based on a 2-D nucleation mechanism could explain the abnormal grain growth behavior. It was also proposed that a densification process is closely related to the interface atomic structure. Enhanced densification by carefully chosen additives during solid state sintering was explained in terms of the grain-boundary structural transition from an ordered to a disordered open structure. [source] Transmission electron microscopy and theoretical analysis of AuCu nanoparticles: Atomic distribution and dynamic behaviorMICROSCOPY RESEARCH AND TECHNIQUE, Issue 7 2006J.A. Ascencio Abstract Though the application of bimetallic nanoparticles is becoming increasingly important, the local atomistic structure of such alloyed particles, which is critical for tailoring their properties, is not yet very clearly understood. In this work, we present detailed study on the atomistic structure of Au,Cu nanoparticles so as to determine their most stable configurations and the conditions for obtaining clusters of different structural variants. The dynamic behavior of these nanoparticles upon local heating is investigated. AuCu nanoparticles are characterized by high resolution transmission electron microscopy (HRTEM) and energy filtering elemental composition mapping (EFECM), which allowed us to study the internal structure and the elemental distribution in the particles. Quantum mechanical approaches and classic molecular dynamics methods are applied to model the structure and to determine the lowest energy configurations, the corresponding electronic structures, and understand structural transition of clusters upon heating, supported by experimental evidences. Our theoretical results demonstrate only the core/shell bimetallic structure have negative heat of formation, both for decahedra and octahedral, and energetically favoring core/shell structure is with Au covering the core of Cu, whose reverse core/shell structure is not stable and may transform back at a certain temperature. Experimental evidences corroborate these structures and their structural changes upon heating, demonstrating the possibility to manipulate the structure of such bimetallic nanoparticles using extra stimulating energy, which is in accordance with the calculated coherence energy proportions between the different configurations. Microsc. Res. Tech., 2006. © 2006 Wiley-Liss, Inc. [source] The role of irregular unit, GAAS, on the secondary structure of Bombyx mori silk fibroin studied with 13C CP/MAS NMR and wide-angle X-ray scatteringPROTEIN SCIENCE, Issue 8 2002Tetsuo Asakura Abstract Bombyx mori silk fibroin is a fibrous protein whose fiber is extremely strong and tough, although it is produced by the silkworm at room temperature and from an aqueous solution. The primary structure is mainly Ala-Gly alternative copolypeptide, but Gly-Ala-Ala-Ser units appear frequently and periodically. Thus, this study aims at elucidating the role of such Gly-Ala-Ala-Ser units on the secondary structure. The sequential model peptides containing Gly-Ala-Ala-Ser units selected from the primary structure of B. mori silk fibroin were synthesized, and their secondary structure was studied with 13C CP/MAS NMR and wide-angle X-ray scattering. The 13C isotope labeling of the peptides and the 13C conformation-dependent chemical shifts were used for the purpose. The Ala-Ala units take antiparallel ,-sheet structure locally, and the introduction of one Ala-Ala unit in (Ala-Gly)15 chain promotes dramatical structural changes from silk I (repeated ,-turn type II structure) to silk II (antiparallel ,-sheet structure). Thus, the presence of Ala-Ala units in B. mori silk fibroin chain will be one of the inducing factors of the structural transition for silk fiber formation. The role of Tyr residue in the peptide chain was also studied and clarified to induce "locally nonordered structure." [source] Groupoid of orientational variantsACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2006Cyril Cayron Daughter crystals in orientation relationship with a parent crystal are called variants. They can be created by a structural phase transition (Landau or reconstructive), by twinning or by precipitation. Internal and external classes of transformations defined from the point groups of the parent and daughter phases and from a transformation matrix allow the orientations of the distinct variants to be determined. These are algebraically identified with left cosets and their number is given by the Lagrange formula. A simple equation links the numbers of variants of the direct and inverse transitions. The equivalence classes on the transformations between variants are isomorphic to the double cosets (operators) and their number is given by the Burnside formula. The orientational variants and the operators constitute a groupoid whose composition table acts as a crystallographic signature of the transition. A general method that determines if two daughter variants can be inherited from more than one parent crystal is also described. A computer program has been written to calculate all these properties for any structural transition; some results are given for Burgers transitions and for martensitic transitions in steels. The complexity, irreversibility and entropy of fractal systems constituted by orientational variants generated by thermal cycling are briefly discussed. [source] The impact of off-market trading on liquidity: Evidence from the Australian options marketTHE JOURNAL OF FUTURES MARKETS, Issue 4 2010Andrew Lepone This study investigates the impact of reducing the contract size threshold for off-market trading on transaction costs in an options market. This study provides evidence that market makers compete more aggressively for small-to-medium trades and quote mid-size depths more often after the regime change. Results also indicate that small-to-medium trades incur lower transaction costs; however, large trades that are executed on the central limit order book do not benefit from the structural transition. Given recent frictions imposed by regulators on equity markets, these results suggest that options markets provide an effective means for investors to replicate short-selling in underlying securities. © 2009 Wiley Periodicals, Inc. Jrl Fut Mark 30:361,377, 2010 [source] Characterization of copper binding to the peptide amyloid-,(1,16) associated with Alzheimer's diseaseBIOPOLYMERS, Issue 1 2006Qing-Feng Ma Abstract Amyloid-, peptide (A,) is the principal constituent of plaques associated with Alzheimer's disease (AD) and is thought to be responsible for the neurotoxicity associated with the disease. Copper binding to A, has been hypothesized to play an important role in the neruotoxicity of A, and free radical damage, and Cu2+ chelators represent a possible therapy for AD. However, many properties of copper binding to A, have not been elucidated clearly, and the location of copper binding sites on A, is also in controversy. Here we have used a range of spectroscopic techniques to characterize the coordination of Cu2+ to A,(1,16) in solution. Electrospray ionization mass spectrometry shows that copper binds to A,(1,16) at pH 6.0 and 7.0. The mode of copper binding is highly pH dependent. Circular dichroism results indicate that copper chelation causes a structural transition of A,(1,16). UV-visible absorption spectra suggest that three nitrogen donor ligands and one oxygen donor ligand (3N1O) in A,(1,16) may form a type II square-planar coordination geometry with Cu2+. By means of fluorescence spectroscopy, competition studies with glycine and L -histidine show that copper binds to A,(1,16) with an affinity of Ka , 107M,1 at pH 7.8. Besides His6, His13, and His14, Tyr10 is also involved in the coordination of A,(1,16) with Cu2+, which is supported by 1H NMR and UV-visible absorption spectra. Evidence for the link between Cu2+ and AD is growing, and this work has made a significant contribution to understanding the mode of copper binding to A,(1,16) in solution. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 20,31, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Spectroscopic study on structure of horseradish peroxidase in water and dimethyl sulfoxide mixtureBIOPOLYMERS, Issue 2 2002Yasushi Maeda Abstract The structure of horseradish peroxidase (HRP) in phosphate buffered saline (PBS)/dimethyl sulfoxide (DMSO) mixed solvents at different compositions is investigated by IR, electronic absorption, and fluorescence spectroscopies. The fluorescence spectra and the amide I spectra of ferric HRP [HRP(Fe3+)] show that overall structural changes are relatively small up to 60% DMSO. Although the amide I band of HRP(Fe3+) shows a gradual change in the secondary structure and a decrease in the contents of , helices, its fluorescence spectra indicate that the distance between the heme and Trp173 is almost constant. In contrast, the changes in the positions of the Soret bands for resting HRP(Fe3+) and catalytic intermediates (compounds I and II) and the IR spectra at the CO stretching vibration mode of carbonyl ferrous HRP [HRP(Fe2+)-CO] show that the microenvironment in the distal heme pocket is altered, even with low DMSO contents. The large reduction of the catalytic activity of HRP even at low DMSO contents can be attributed to the structural transition in the distal heme pocket. In PBS/DMSO mixtures containing more than 70 vol % DMSO, HRP undergoes large structural changes, including a large loss of the secondary structure and a dissociation of the heme from the apoprotein. The presence of the components of the amide I band that can be assigned to strongly hydrogen bonding amide CO groups at 1616 and 1684 cm,1 suggests that the denatured HRP may aggregate through strong hydrogen bonds. © 2002 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 67: 107,112, 2002 [source] Metal Binding Properties of Fluorescent Analogues of Trichogin GA,IV: A Conformational Study by Time-Resolved Spectroscopy and Molecular Mechanics InvestigationsCHEMBIOCHEM, Issue 1 2009Mariano Venanzi Prof. Abstract The metal ion binding properties of two fluorescent analogues of trichogin GA,IV, which is a natural undecapeptide showing significant antimicrobial activity, were studied by circular dichroism, time-resolved optical spectroscopy, and molecular mechanics calculations. Binding of CaII and GdIII to the peptides investigated was shown to promote a structural transition from highly helical conformations to folded structures characterized by formation of a loop that embedded the metal ion. Time-resolved spectroscopy revealed that peptide dynamics is also remarkably affected by ion binding: peptide-backbone motions slowed down to the microsecond time scale. Finally, molecular mechanics calculations emphasized the role of the central Gly5-Gly6 motif, which allowed for the twisting of the peptide segment that gave rise to the formation of the binding cavity. [source] Transitions of serum albumin in patients with glomerulosclerosis ,in vivo' characterization by electrophoretic titration curvesELECTROPHORESIS, Issue 14 2006Maurizio Bruschi Abstract HSA functions as a physiological transporter of solutes and small molecules that induce structural transitions ,in vitro'. Analysis of these transitions requires prior purification of HSA that could introduce bias due to conformational changes. We utilized electrophoretic titration curves to describe a neutral to acid (N,A) transition of HSA directly in sera of seven patients with active focal segmental glomerulosclerosis (FSGS). The divergent electrophoretic profile of HSA was characterized by a shift in the range of pHs between 4.5 and 7.5 with an average variation of free electrophoretic mobility corresponding to loss of 1 positive charge in the pKa protonation range of histidyl residues and should involve domain I of HSA. ,In-gel' determination by maleimide-PEO2-biotin of free SH 34 of domain I showed inaccessibility of the dye at this site in pathological HSA and alkylation with the same complex induced N,A transition in normal HSA. Potential binders of free imidazoles such as Ca++ and/or of SH 34 such as NO were excluded on the basis of direct titration and studies on binding stimulation. This is the first report describing a transition of HSA directly ,in vivo', and the utilization of electrophoretic titration curves was critical to this purpose. This transition appears to be specific to FSGS and is unrelated to the nephrotic syndrome, Ca++ and NO binding. Spectroscopic analysis will elucidate the structural implication. [source] Raman microspectroscopic study on low-pH-induced DNA structural transitions in the presence of magnesium ionsJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2002C. M. Muntean Low-pH-induced DNA structural changes were investigated in the pH range 6.8,2.10 by Raman microspectroscopy. Measurements were carried out on calf thymus DNA in the presence of low concentrations of Mg2+ ions. Vibrational spectra are presented in the wavenumber region 500,1650 cm,1. Large changes in the Raman spectra of calf-thymus DNA were observed on lowering the pH value. These are due to protonation and unstacking of the DNA bases during DNA melting and also to changes in the DNA backbone conformation. The intensities of the Raman bands of guanine (681 cm,1), adenine (728 cm,1), thymine (752 cm,1) and cytosine (785 cm,1), typical of the C2,- endo - anti conformation of B-DNA, are discussed. The B-form marker near 835 cm,1 and the base vibrations in the higher wavenumber region (1200,1680 cm,1) are analysed. Effects of low pH value upon the protonation mechanism of opening AT and changing the protonation of GC base pairs in DNA are discussed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Raman and Infrared Imaging of Dynamic Polymer SystemsMACROMOLECULAR MATERIALS & ENGINEERING, Issue 7 2007Jack L. Koenig Abstract This work reviews principles of Raman and infrared imaging, as well as applications of the art to understand physiochemical phenomena in polymer systems. Image sequences may be assessed in terms of spatial or spectral changes that occur over time, either within a specific region or across the field of view. As such, the methods have enabled the analysis of diffusion and dissolution processes at polymer interfaces, drug release from polymer matrices, and structural transitions among others. Despite analytical limitations imposed by resolution (spectral or spatial) and sample preparation, Raman and infrared imaging are powerful tools for relating performance attributes to molecular-level characteristics. [source] Mechanochemical ATPases and transcriptional activationMOLECULAR MICROBIOLOGY, Issue 4 2002X. Zhang Summary Transcriptional activator proteins that act upon the ,54 -containing form of the bacterial RNA polymerase belong to the extensive AAA+ superfamily of ATPases, members of which are found in all three kingdoms of life and function in diverse cellular processes, often via chaperone-like activities. Formation and collapse of the transition state of ATP for hydrolysis appears to engender the interaction of the activator proteins with ,54 and leads to the protein structural transitions needed for RNA polymerase to isomerize and engage with the DNA template strand. The common oligomeric structures of AAA+ proteins and the crea-tion of the active site for ATP hydrolysis between protomers suggest that the critical changes in protomer structure required for productive interactions with ,54 -holoenzyme occur as a consequence of sensing the state of the , -phosphate of ATP. Depending upon the form of nucleotide bound, different functional states of the activator are created that have distinct substrate and chaperone-like binding activ-ities. In particular, interprotomer ATP interactions rely upon the use of an arginine finger, a situation reminiscent of GTPase-activating proteins. [source] Pressure-induced structural transitions in multi-walled carbon nanotubesPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 10 2009Hiroyuki Shima Abstract We demonstrate a novel cross-sectional deformation, called the radial corrugation, of multi-walled carbon nanotubes (MWNTs) under hydrostatic pressure. Theoretical analyses based on the continuum elastic approximation have revealed that MWNTs consisting of more than ten concentric walls undergo elastic deformations at critical pressure , above which the circular shape of the cross-section becomes radially corrugated. Various corrugation modes have been observed by tuning the innermost tube diameter and the number of constituent walls, which is a direct consequence of the core,shell structure of MWNTs. Cross-sectional views of MWNT under high hydrostatic pressure: elliptic deformation with the mode index n,=,2 (left), and radial corrugations with n,=,5 (center), and n,=,6 (right). The index n indicates the circumferential wave number of the deformed cross-section. [source] G-mode behaviour of closed ended single wall carbon nanotubes under pressurePHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 3 2009Ahmad J. Ghandour Abstract We have performed high pressure Raman experiments on closed-ended single wall carbon nanotubes using two different excitation wavelengths: 632.8 nm and 514 nm. We found that the shape of the G-mode spectrum changes while changing the excitation wavelength at lower pressures, while it becomes similar at 3.5 GPa. In addition we record that the value of the transition pressure, associated with the structural transitions in the tubes, has also changed with changing the excitation wavelength even though we are examining tubes from the same produced sample. We attribute these results to the tubes having different electronic nature (metallic; semi-conducting) and different diameters in resonance with each excitation wavelength. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Ultrafast X-ray diffraction in liquid, solution and gas: present status and future prospectsACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010Jeongho Kim In recent years, the time-resolved X-ray diffraction technique has been established as an excellent tool for studying reaction dynamics and protein structural transitions with the aid of 100,ps X-ray pulses generated from third-generation synchrotrons. The forthcoming advent of the X-ray free-electron laser (XFEL) will bring a substantial improvement in pulse duration, photon flux and coherence of X-ray pulses, making time-resolved X-ray diffraction even more powerful. This technical breakthrough is envisioned to revolutionize the field of reaction dynamics associated with time-resolved diffraction methods. Examples of candidates for the first femtosecond X-ray diffraction experiments using highly coherent sub-100,fs pulses generated from XFELs are presented in this paper. They include the chemical reactions of small molecules in the gas and solution phases, solvation dynamics and protein structural transitions. In these potential experiments, ultrafast reaction dynamics and motions of coherent rovibrational wave packets will be monitored in real time. In addition, high photon flux and coherence of XFEL-generated X-ray pulses give the prospect of single-molecule diffraction experiments. [source] Increased aggregation propensity of IgG2 subclass over IgG1: Role of conformational changes and covalent character in isolated aggregatesPROTEIN SCIENCE, Issue 9 2010Heather Franey Abstract Aggregation of human therapeutic antibodies represents a significant hurdle to product development. In a test across multiple antibodies, it was observed that IgG1 antibodies aggregated less, on average, than IgG2 antibodies under physiological pH and mildly elevated temperature. This phenomenon was also observed for IgG1 and IgG2 subclasses of anti-streptavidin, which shared 95% sequence identity but varied in interchain disulfide connectivity. To investigate the structural and covalent changes associated with greater aggregation in IgG2 subclasses, soluble aggregates from the two forms of anti-streptavidin were isolated and characterized. Sedimentation velocity analytical ultracentrifugation (SV-AUC) measurements confirmed that the aggregates were present in solution, and revealed that the IgG1 aggregate was composed of a predominant species, whereas the IgG2 aggregate was heterogeneous. Tertiary structural changes accompanied antibody aggregation as evidenced by greater ANS (8-Anilino-1-naphthalene sulfonic acid) binding to the aggregates over monomer, and differences in disulfide character and tryptophan environments between monomer, oligomer and aggregate species, as observed by near-UV circular dichroism (CD). Differences between subclasses were observed in the secondary structural changes that accompanied aggregation, particularly in the intermolecular ,-sheet and turn structures between the monomer and aggregate species. Free thiol determination showed ,2.4-fold lower quantity of free cysteines in the IgG1 subclass, consistent with the 2.4-fold reduction in aggregation of the IgG1 form when compared with IgG2 under these conditions. These observations suggested an important role for disulfide bond formation, as well as secondary and tertiary structural transitions, during antibody aggregation. Such degradations may be minimized using appropriate formulation conditions. [source] Modulation of protein aggregation by polyethylene glycol conjugation: GCSF as a case studyPROTEIN SCIENCE, Issue 5 2006Rahul S. Rajan Abstract Polyethylene glycol (PEG) conjugation to proteins has emerged as an important technology to produce drug molecules with sustained duration in the body. However, the implications of PEG conjugation to protein aggregation have not been well understood. In this study, conducted under physiological pH and temperature, N-terminal attachment of a 20 kDa PEG moiety to GCSF had the ability to (1) prevent protein precipitation by rendering the aggregates soluble, and (2) slow the rate of aggregation relative to GCSF. Our data suggest that PEG-GCSF solubility was mediated by favorable solvation of water molecules around the PEG group. PEG-GCSF appeared to aggregate on the same pathway as that of GCSF, as evidenced by (a) almost identical secondary structural transitions accompanying aggregation, (b) almost identical covalent character in the aggregates, and (c) the ability of PEG-GCSF to rescue GCSF precipitation. To understand the role of PEG length, the aggregation properties of free GCSF were compared to 5kPEG-GCSF and 20kPEG-GCSF. It was observed that even 5kPEG-GCSF avoided precipitation by forming soluble aggregates, and the stability toward aggregation was vastly improved compared to GCSF, but only marginally less stable than the 20kPEG-GCSF. Biological activity measurements demonstrated that both 5kPEG-GCSF and 20kPEG-GCSF retained greater activity after incubation at physiological conditions than free GCSF, consistent with the stability measurements. The data is most compatible with a model where PEG conjugation preserves the mechanism underlying protein aggregation in GCSF, steric hindrance by PEG influences aggregation rate, while aqueous solubility is mediated by polar PEG groups on the aggregate surface. [source] Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopyBIOPOLYMERS, Issue 1 2006Lydie Grajcar Abstract We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl, and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n , (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6,28, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Crystal Structures and Characterizations of Bis (pyrrolidinedithiocarbamato) Cu(II) and Zn(II) ComplexesCHINESE JOURNAL OF CHEMISTRY, Issue 1 2003Jian Fang-Fang Abstract The structures of [Cu (S2CN (CH2)4)2] (1) and [Zn2(S2CN-(CH2)4)4] (2) have been determined by X-ray crystallography analysis. They are all isomorphous and triclinic, space group of P1,, with Z = 1. The lattice parameters of compound 1 is: a = 0.63483(2) nm, b = 0.74972(3) nm, c=0.78390(1) mn, , = 75.912(2)°, , = 78.634(2)° and , = 86.845(2)°; compound 2: a = 0.78707(6) nm, b=0.79823(6) nm, c = 1.23246(9) nm, , = 74.813(2)°, , = 73.048(2)° and , = 88.036(2)°. The copper atom is located on a crystallographic inversion center and zinc atom lies across centers of symmetry. The Cu(II) ion has a square-planar geometry while Zn(II) has a distorted tetrahedral geometry. The thermal gravity (TG) data indicate that no structural transitions in the two compounds were abserved and the decomposition products can adsorb gas. Also they all have a high thermal stability. [source] | ||||||||||||||||||||||||||||||||||