Relationship between prion propensity and the rates of individual molecular steps of fibril assembly.

Peptides and proteins possess an inherent propensity to self-assemble into generic fibrillar nanostructures known as amyloid fibrils, some of which are involved in medical conditions such as Alzheimer disease. In certain cases, such structures can self-propagate in living systems as prions and transmit characteristic traits to the host organism. The mechanisms that allow certain amyloid species but not others to function as prions are not fully understood. Much progress in understanding the prion phenomenon has been achieved through the study of prions in yeast as this system has proved to be experimentally highly tractable; but quantitative understanding of the biophysics and kinetics of the assembly process has remained challenging. Here, we explore the assembly of two closely related homologues of the Ure2p protein from Saccharomyces cerevisiae and Saccharomyces paradoxus, and by using a combination of kinetic theory with solution and biosensor assays, we are able to compare the rates of the individual microscopic steps of prion fibril assembly. We find that for these proteins the fragmentation rate is encoded in the structure of the seed fibrils, whereas the elongation rate is principally determined by the nature of the soluble precursor protein. Our results further reveal that fibrils that elongate faster but fracture less frequently can lose their ability to propagate as prions. These findings illuminate the connections between the in vitro aggregation of proteins and the in vivo proliferation of prions, and provide a framework for the quantitative understanding of the parameters governing the behavior of amyloid fibrils in normal and aberrant biological pathways.

Molecular/Cluster Statistical Thermodynamics Methods To Simulate Quasi-Static Deformations At Finite Temperature

The rapid evolution of nanotechnology appeals for the understanding of global response of nanoscale systems based on atomic interactions, hence necessitates novel, sophisticated, and physically based approaches to bridge the gaps between various length and time scales. In this paper, we propose a group of statistical thermodynamics methods for the simulations of nanoscale systems under quasi-static loading at finite temperature, that is, molecular statistical thermodynamics (MST) method, cluster statistical thermodynamics (CST) method, and the hybrid molecular/cluster statistical thermodynamics (HMCST) method. These methods, by treating atoms as oscillators and particles simultaneously, as well as clusters, comprise different spatial and temporal scales in a unified framework. One appealing feature of these methods is their "seamlessness" or consistency in the same underlying atomistic model in all regions consisting of atoms and clusters, and hence can avoid the ghost force in the simulation. On the other hand, compared with conventional MD simulations, their high computational efficiency appears very attractive, as manifested by the simulations of uniaxial compression and nanoindenation. (C) 2008 Elsevier Ltd. All rights reserved.

Reaction of glucose catalyzed by framework and extraframework tin sites in zeolite beta

The isomerization of glucose into fructose is a large-scale reaction for the production of high-fructose corn syrup, and is now being considered as an intermediate step in the possible route of biomass conversion into fuels and chemicals. Recently, it has been shown that a hydrophobic, large pore, silica molecular sieve having the zeolite beta structure and containing framework Sn⁴⁺ (Sn-Beta) is able to isomerize glucose into fructose in aqueous media. Here, I have investigated how this catalyst converts glucose to fructose and show that it is analogous to that achieved with metalloenzymes. Specifically, glucose partitions into the molecular sieve in the pyranose form, ring opens to the acyclic form in the presence of the Lewis acid center (framework Sn⁴⁺), isomerizes into the acyclic form of fructose and finally ring closes to yield the furanose product. Akin to the metalloenzyme, the isomerization step proceeds by intramolecular hydride transfer from C2 to C1. Extraframework tin oxides located within hydrophobic channels of the molecular sieve that exclude liquid water can also isomerize glucose to fructose in aqueous media, but do so through a base-catalyzed proton abstraction mechanism. Extraframework tin oxide particles located at the external surface of the molecular sieve crystals or on amorphous silica supports are not active in aqueous media but are able to perform the isomerization in methanol by a base-catalyzed proton abstraction mechanism. Post-synthetic exchange of Na⁺ with Sn-Beta alters the glucose reaction pathway from the 1,2 intramolecular hydrogen shift (isomerization) to produce fructose towards the 1,2 intramolecular carbon shift (epimerization) that forms mannose. Na⁺ remains exchanged onto silanol groups during reaction in methanol solvent, leading to a near complete shift in selectivity towards glucose epimerization to mannose. In contrast, decationation occurs during reaction in aqueous solutions and gradually increases the reaction selectivity to isomerization at the expense of epimerization. Decationation and concomitant changes in selectivity can be eliminated by addition of NaCl to the aqueous reaction solution. Thus, framework tin sites with a proximal silanol group are the active sites for the 1, 2 intramolecular hydride shift in the isomerization of glucose to fructose, while these sites with Na-exchanged silanol group are the active sites for the 1, 2 intramolecular carbon shift in epimerization of glucose to mannose.

The separation of atomic and molecular gases from helium by cataphoresis

The cataphoretic purification of helium was investigated for binary mixtures of He with Ar, Ne, N₂, O₂, CO, and CO₂ in DC glow discharge. An experimental technique was developed to continuously measure the composition in the anode end-bulb without sample withdrawal. Discharge currents ranged from 10 ma to 100 ma. Total gas pressure ranged from 2 torr to 9 torr. Initial compositions of the minority component in He ranged from 1.2 mole percent to 7.5 mole percent.

The cataphoretic separation of Ar and Ne from He was found to be in agreement with previous investigators. The cataphoretic separation of N₂, O₂, and CO from He was found to be similar to noble gas systems in that the steady-state separation improved with (1) increasing discharge current, (2) increasing gas pressure, and (3) decreasing initial composition of the minority component. In the He-CO₂ mixture, the CO₂ dissociated to CO plus O₂. The fraction of CO₂ dissociated was directly proportional to the current and pressure and independent of initial composition.

The experimental results for the separation of Ar, Ne, N₂, O₂, and CO from He were interpreted in the framework of a recently proposed theoretical model involving an electrostatic Peclet number. In the model the electric field was assumed to be constant. This assumption was checked experimentally and the maximum variation in electric field was 35% in time and 30% in position. Consequently, the assumption of constant electric field introduced no more than 55% variation in the electrostatic Peclet number during a separation.

To aid in the design of new cataphoretic systems, the following design criteria were developed and tested in detail: (1) electric field independent of discharge current, (2) electric field directly proportional to total pressure, (3) ion fraction of impurity directly proportional to discharge current, and (4) ion fraction of impurity independent of total pressure. Although these assumptions are approximate, they enabled the steady-state concentration profile to be predicted to within 25% for 75% of the data. The theoretical model was also tested with respect to the characteristic time associated with transient cataphoresis. Over 80% of the data was within a factor of two of the calculated characteristic times.

The electrostatic Peclet number ranged in value from 0.13 to 4.33. Back-calculated ion fractions of the impurity component ranged in value from 4.8x10^-6 to 178x10^-6.

Local Frustration Determines Molecular and Macroscopic Helix Structures

The effect of displaying cytochromes from an amyloid fibre is modelled as perturbation of -strands in a bilayer of helical -sheets, thereby explaining the spiral morphology of decorated amyloid and the dynamic response of morphology to cytochrome conformation. The morphology of the modelled fibre, which consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting units, depends primarily on the rigid constraints between units rather than the soft interactions between them. The framework is a discrete version of the bilayered frustration principle that drives morphology in Bauhinia seedpods. We show that self-assembly of frustrated long range structures can occur if the building blocks themselves are internally frustrated, e.g. amyloid morphology is governed by the conformation of the misfolded protein nucleating the fibre. Our model supports the idea that any peptide sequence can form amyloid if bilayers can form first, albeit stabilised by additional material such as chaperones or cytochromes. Analysis of experimentally derived amyloid structures supports our conclusions and suggests a range of frustration effects, which natural amyloid fibres may exploit. From this viewpoint, amyloid appears as a molecular example of a more general universal bilayered frustration principle, which may have profound implications for materials design using fibrous systems. Our model provides quantitative guidance for such applications. The relevance to longer length scales was proved by designing the morphology of a series of macroscopic magnetic stacks. Finally, this work leads to the idea of mixing controlled morphologically defined species to generate higher-order assembly and complex functional behaviour. The systematic kinking of decorated fibres and the nested frustration of the Bauhinia seed pod are two outstanding examples.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

Characterization of metal-containing molecular sieves and their catalytic properties in the selective oxidation of cyclohexane

Three types of metal-containing molecular sieves with AFI, AEL and CHA structures (Me = Co, Mn, Cr and V) were synthesized hydrothermally and characterized by XRD, XRF, TG, TPR, NH3-TPD and FT-IR. It was revealed that metals were incorporated into the framework of molecular sieves and induced the presence of charge centers. Both cobalt and manganese in the framework of AIPO-5, AlPO-11 and SAPO-34 were not reducible before the structure collapse. The redox behaviours of these catalysts in cyclohexane oxidation at 403 K using O-2 as oxidant were examined. CoAPO-11 exhibited best activity and good selectivities for the monofunctional oxidation products (88.5%). Cyclohexanol was the major product over most catalysts, whereas for Cr-containing molecular sieves, high selectivity of cyclohexanone was observed. Investigation of reaction mechanism based on CoAPO-11 and CrAPO-5 catalysts indicated that the decomposition of cyclohexyl hydroperoxide (CHHP), the intermediate in cyclohexane oxidation, followed the pathway: cyclohexanone <-- CHHP --> cyclohexanol -->cyclohexanone. (C) 2004 Elsevier B.V. All rights reserved.

Identifying the isolated transition metal ions/oxides in molecular sieves and on oxide supports by UV resonance Raman spectroscopy

Isolated transition metal ions/oxides in molecular sieves and on surfaces are a class of active sites for selective oxidation of hydrocarbons. Identifying the active sites and their coordination structure is vital to understanding their essential role played in catalysis and designing and synthesizing more active and selective catalysts. The isolated transition metal ions in the framework of molecular sieves (e.g., TS-1, Fe-ZSM-5, and V-MCM-41) or on the surface of oxides (e.g., MoO3/Al2O3 and TiO2/SiO2) were successfully identified by UV resonance Raman spectroscopy. The charge transfer transitions between the transition metal ions and the oxygen anions are excited by a UV laser and consequently the UV resonance Raman effect greatly enhances the Raman signals of the isolated transition metal ions. The local coordination of these ions in the rigid framework of molecular sieves or in the relatively flexible structure on the surface can also be differentiated by the shifts of the resonance Raman bands. The relative concentration of the isolated transition metal ion/oxides could be estimated by the intensity ratio of Raman bands. This study demonstrates that the UV resonance Raman spectroscopy is a general technique that can be widely applied to the in-situ characterization of catalyst synthesis and catalytic reactions. (C) 2003 Elsevier Science (USA). All rights reserved.

Guest inducing p-sulfonatocalix[4] arene into three-dimensional capsule architecture and a mixed A-B double layer framework

The reactions of sodium p-sulfonatocalix[4]arene (Na5L) and terbium/europium(III) chloride in the presence of pyrazine-N,N'-dioxide (PNNO) in aqueous solutions gave the crystalline complexes 1 and 2. Both structures contain molecular capsules of p-sulfonatocalix[4] arene with PNNO as guest molecules in the cavity of the calix[4]arenes. The molecular capsules are connected through sodium and terbium (or europium) centers forming a three-dimensional framework.

Anion coordination and molecular assembly in C2-substituted thiamine-anion systems: effects of the anion and molecular conformation

The compounds (het)(PtCl6)2H(2)O 1, (het)(HgI4).H2O 2 (het = 2-(alpha-hydroxyethyl)thiamine) and (hpt)(Hg2Br6) 3 (hpt = 2-(alpha-hydroxypropyl)thiamine) have been prepared and structurally characterized by X-ray crystallography in order to study the influence of the anion and molecular conformation on the formation of supramolecular architectures that adsorb anionic species. Both het and hpt molecules adopt the usual S conformation for C2-substituted thiamine but differ from the F conformation for C2-free thiamine derivatives. Two types of characteristic ligand-anion complexation are observed, being of the forms C(6')-H...anion...thiazolium-ring (in 1 and 2) and N(4'1)-H...anion...thiazolium-ring (in 3). The reaction of het with PtCl62- or HgI42- gives a 1-D double-chain in 1, consisting of two hydrogen-bonded het chains, which are cross-linked by anions through hydrogen bonding and anion...aromatic-ring interactions, or a cationic 3-D framework in 2 formed by the stacking of hydrogen-bonded sheets with anion-and-water-filled channels. In the case of 3, hydrogen-bonded hpt dimers and HgBr62- anions form alternate cation-anion columns. A comparison with the cases of C2-free thiamine-anion complexes indicates that the change in molecular conformation results in novel supramolecular assemblies in 1 and 2 and an analogous architecture in 3, which also depends on the nature of the anions.

What has brought on the effects of number-average molecular weight on the spinodals in polymer mixtures?

On the basis of the thermodynamics of Gibbs, the spinodal for the quasibinary system was derived in the framework of the Sanchez-Lacombe lattice fluid theory. All of the spinodals were calculated based on a model polydisperse polymer mixture, where each polymer contains three different molecular weight subcomponents. According to our calculations, the spinodal depends on both weight-average ((M) over bar (w)) and number-average ((M) over bar (n)) molecular weights, whereas that of the z-average molecular weight is invisible. Moreover, the extreme of the spinodal decreases when the polydispersity index (eta = (M) over bar (w)/(M) over bar (n)) of the polymer increases. The effect of polydispersity on the spinodal decreases when the molecular weight gets larger and can be negligible at a certain large molecular weight. It is well-known that the influence of polydispersity on the phase equilibrium (coexisting curve, cloud point curves) is much more pronounced than on the spinodal. The effect of M, on the spinodal is discussed as it results from the infuluence of composition temperatures, molecular weight, and the latter's distribution on free volume. An approximate expression, which is in the assumptions of v* v(1)* = v(2)* and 1/r --> 0 for both of the polymers, was also derived for simplification. It can be used in high molecular weight, although it failed to make visible the effect of number-average molecular weight on the spinodal.

Identifying framework titanium in TS-1 zeolite by UV resonance Raman spectroscopy

Framework titanium in Ti-silicalite-1 (TS-1) zeolite was selectively identified by its resonance Raman bands using ultraviolet (W) Raman spectroscopy. Raman spectra of the TS-1 and silicalite-1 zeolites were obtained and compared using continuous wave laser lines at 244, 325, and 488 nm as the excitation sources. It was only with the excitation at 244 nm that resonance enhanced Raman bands at 490, 530, and 1125 cm(-1) appeared exclusively for the TS-1 zeolite. Furthermore, these bands increased in intensity with the crystallization time of the TS-1 zeolite. The Raman bands at 490, 530, and 1125 cm(-1) are identified as the framework titanium species because they only appeared when the laser excites the charge-transfer transition of the framework titanium species in the TS-1. No resonance Raman enhancement was detected for the bands of silicalite-1 zeolite and for the band at 960 cm(-1) of TS-1 with any of the excitation sources ranging from the visible tb UV regions. This approach can be applicable for the identification of other transition metal ions substituted in the framework of a zeolite or any other molecular sieve.

Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod

Van den Berg, A. W. C., Flikkema, E., Lems, S., Bromley, S. T., Jansen, J. C. (2006). Molecular dynamics-based approach to study the anisotropic self-diffusion of molecules in porous materials with multiple cage types: Application to H-2 in losod. Journal of physical chemistry b, 110 (1), 501-506. RAE2008

Elucidating the Molecular Composition of Cartilage by Proteomics.

Articular cartilage consists of chondrocytes and two major components, a collagen-rich framework and highly abundant proteoglycans. Most prior studies defining the zonal distribution of cartilage have extracted proteins with guanidine-HCl. However, an unextracted collagen-rich residual is left after extraction. In addition, the high abundance of anionic polysaccharide molecules extracted from cartilage adversely affects the chromatographic separation. In this study, we established a method for removing chondrocytes from cartilage sections with minimal extracellular matrix protein loss. The addition of surfactant to guanidine-HCl extraction buffer improved protein solubility. Ultrafiltration removed interference from polysaccharides and salts. Almost four-times more collagen peptides were extracted by the in situ trypsin digestion method. However, as expected, proteoglycans were more abundant within the guanidine-HCl extraction. These different methods were used to extract cartilage sections from different cartilage layers (superficial, intermediate, and deep), joint types (knee and hip), and disease states (healthy and osteoarthritic), and the extractions were evaluated by quantitative and qualitative proteomic analyses. The results of this study led to the identifications of the potential biomarkers of osteoarthritis (OA), OA progression, and the joint specific biomarkers.

Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia

The high-temperature cubic-tetragonal phase transition of pure stoichiometric zirconia is studied by molecular dynamics (MD) simulations and within the framework of the Landau theory of phase transformations. The interatomic forces are calculated using an empirical, self-consistent, orthogonal tight-binding model, which includes atomic polarizabilities up to the quadrupolar level. A first set of standard MD calculations shows that, on increasing temperature, one particular vibrational frequency softens. The temperature evolution of the free-energy surfaces around the phase transition is then studied with a second set of calculations. These combine the thermodynamic integration technique with constrained MD simulations. The results seem to support the thesis of a second-order phase transition but with unusual, very anharmonic behavior above the transition temperature.