Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

不同活化剂对石油焦基活性炭孔结构的影响

以石油焦为原料 ,Na OH,KOH和 Na2 CO3 为活化剂制备活性炭 ,采用氮气吸附考察了不同活化剂对活性炭的比表面积、中孔和微孔孔径分布、孔容积及平均孔径等孔结构的影响 .结果表明 :KOH活化制备的活性炭包含 1 nm的微孔和 4nm的中孔 ,总孔容 0 .648cm3 /g,比表面积大 ;Na OH制备的活性炭以 1 nm的微孔为主 ,占总孔容 ( 0 .1 65 cm3 /g)的 98% ,平均孔径 1 .83nm;Na2 CO3 制备的活性炭以 4nm的中孔为主 ,占总孔容 ( 0 .1 43cm3 /g)的 68.5 % ,平均孔径 3.42 nm,比表面积小 .3种样品的孔径都呈现出多峰分布特征 .KOH和 Na2 CO3 活化制备的活性炭的 N2 吸附脱附曲线属于 型 ,Na OH活化制备的活性炭吸附脱附曲线属于 型 .     

Structure development in amorphous starch as revealed by X‐ray scattering: Influence of the network structure and water content

The evolution of the amorphous structure of starch was characterized during the drying process by real‐time X‐ray wide‐angle scattering. The X‐ray diffractograms of injection‐molded starch show two superposed, rather broad, scattering maxima indicative of noncrystalline structures. The location of the two peaks has been associated to disordered starch single helices. A third maximum that arises upon drying the material in vacuum is associated to the scattering emerging from regions containing double helices. A model for the starch network is proposed, assuming a primary and a secondary component. The wider, temperature stable component appearing first, is correlated to the entanglement network of the melt. The narrower network component, which is created later, at lower temperature (secondary network), is explained by the formation of double helix regions that densify the wider primary network. The secondary network is increased strongly by the drying process. X‐ray experiments performed during the penetration of water, provoking a higher molecular mobility, reveal a better‐packed helical structure that becomes the precursor of a double helix crystalline formation. When temperature increases, the secondary network is dissolved and water molecules arrange themselves in better‐organized crystals as strongly bound crystal water. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1880–1886, 2006     

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

A 3-D model of a protein can be constructed from its amino acidsequence and the 3-D structures of one or more homologues byannealing three sets of fragments: the structurally conservedregions, structurally variable regions and the side chains.The method encoded in the computer program COMPOSER was assessedby generating 3-D models of eight proteins whose crystal structuresare already known and for which 3-D structures of homologuesare available. In the structurally conserved regions, differencesbetween modelled and X-ray structures are smaller than the differencesbetween the X-ray structures of the modelled protein and thehomologues used to build the model. When several homologuesare used, the contributions of the known structures are weighted,preferably by the square of sequence similarity; this is especiallyimportant when the similarities of the homologues to the modelledstructure differ greatly. The ‘collar’ extensionapproach, in which a similar region of different length in ahomologue is used to extend the framework, can result in a moreaccurate model. If known homologues comprise more than one relatedgroup of proteins and they are both distantly related to theunknown, then alignment of the sequence to be modelled witheach group of homologues facilitates identification of structurallyconserved regions of the unknown and leads to an improved model.Models have root mean square differences (r.m.s.d.s) with thestructures defined by X-ray analysis of between 0.73 and 1.56Å for all C atoms, for seven of the eight models. Forthe model of mucor pepsin, where the closest homologue has 33%sequence identity and 20% of the residues are in structurallyvariable regions, the r.m.s.d. for the framework region is 1.71Å and the r.m.s.d. for all C atoms is 3.47 Â.     

New catalyst systems for the polymerization of acetylene

The catalytic activities of WCI₆Ph₄Sn, MoCl₅Ph₄Sn and tetrabenzyltitanium were examined in the polymerization of acetylene. The structure, morphology and electrical conductivity of the doped and non doped polyacetylene were also studied.     

Platinum particle size effect on the oxidative dehydrogenation of aqueous ethanol

The effect of the platinum particle size was investigated for the catalytic oxidative dehydrogenation of aqueous ethanol to ethanal at a temperature of 303 K, an ethanol concentration of 260 mol m^–3, a partial oxygen pressure 60 kPa, a pH of 9, and an ethanal and ethanoate concentration of 20 mol m^–3. A particle size effect on the turnover frequency was observed but only for particle sizes smaller than 2 nm. Hence, the reaction shows a limited structure sensitivity.     

Molecular association complex of urea with polyethylene: 3. Structural studies of the complex

The crystal structure of urea-polyethylene complex in the hexagonal form, obtained by one of our preparation methods, is analysed by X-ray power diffractometry. In this analysis, the fixed molecular parameters of urea are used, and three models with respect to rotational disorder of the guest polyethylene molecule are assumed. It is shown that the host lattice structure constructed by urea molecules is essentially the same as that of urea-n-paraffin complex. Effects of the disorder structure of the guest on X-ray scattering of the complex are presented. However, there is a difficulty in identifying the disorder structure by X-ray analysis. With the aid of a potential energy calculation between the hexagonal urea tunnel and the guest molecule, a rotational disorder model is preferred.     

Mathematical models of the thermal decomposition of coal: 3. Density,porosity and contraction behaviour

Mathematical models are proposed to predict the true density of coal, semi-coke and coke and the porosity of a coke oven charge during carbonization. These models are combined in a further model which predicts the hitherto unexplained ‘twin-peaked’ contraction curve observed for semi-coke. It is found that the first contraction peak results from the relatively high rate of mass loss occurring towards the end of the primary devolatilization stage. The second peak occurs because of the increase in true density arising from the elimination of hydrogen from the semi-coke.     

COMPUTER SIMULATION OF HYDRODEMETALLATION IN FIXED-BED REACTORS

An isothermal model for hydrodemetallation (HDM) of crude oils in catalytic fixed-bed reactors is proposed. This model involves a consecutive reaction mechanism, which is capable of accounting for particle deposit profiles with interior maxima. Consistent with the fact that HDM catalysts are conglomerates formed by precipitation, the porous catalyst itself is modeled as randomly overlapping spheres of equal size. The metal is deposited as growing metal sulfide crystallites on the inner surface of the catalyst. These crystallites originate from a certain number of randomly scattered nuclei and increase in size as the deposition proceeds. The random sphere model for the catalyst and the deposit provides the changes in the catalyst pore structure—local porosity and surface area.

The mass transport within the domain of the particle is due to restricted liquid diffusion, since the diameter of the metal bearing compound (porphyrin) and the intermediate are comparable to the pore size. The diffusion restrictions taken into account are the enhanced drag imposed on a molecule by adjacent pore walls and steric partitioning.

Since the deposition process is much slower than diffusion and reaction, the pseudo-steady-state assumption can be justified. The equations of conservation for mass are solved by orthogonal collocation on finite elements. Based on this solution technique a computer simulation program of HDM is designed that allows two modes of operation: constant temperature and constant conversion. The simulation program “SIMULA” is highly flexible with regard to reaction kinetics, catalyst structure, reactor design, and operating conditions. In comparison to a base case with uniform activity, the effect of intraparticle (radial) and bed (axial) activity profiles on the conversion rate is discussed. For the case investigated, a radial distribution of activity higher at the center of the particle than at the edge can increase catalyst life by 25%, but axial distribution was less successful.     

Aspects of gasification and structure in cokes from coals

Cokes were prepared from nine coals of different rank and characterized by surface area measurement, reactivity to carbon dioxide at 1473K and Raman-laser spectroscopy. Rates of gasification of cokes on a unit surlface area basis (K¹ = g m^?2 min^?1) decreased with increasing rank of parent coal based on maximum oil reflectances. However rates of gasification could not be related to coke structure as measured by Raman-laser spectroscopy.