Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of proteinmononucleotide complexes

In order to search for a common structural motif in the phosphate-bindingsites of protein–mononucleotide complexes, we investigatedthe structural variety of phosphate-binding schemes by an all-against-allcomparison of 491 binding sites found in the Protein Data Bank.We found four frequently occurring structural motifs composedof protein atoms interacting with phosphate groups, each ofwhich appears in different protein superfamilies with differentfolds. The most frequently occurring motif, which we call thestructural P-loop, is shared by 13 superfamilies and is characterizedby a four-residue fragment, GXXX, interacting with a phosphategroup through the backbone atoms. Various sequence motifs, includingWalker's A motif or the P-loop, turn out to be a structuralP-loop found in a few specific superfamilies. The other threemotifs are found in pairs of superfamilies: protein kinase andglutathione synthetase ATPase domain like, actin-like ATPasedomain and nucleotidyltransferase, and FMN-linked oxidoreductaseand PRTase.     

Benzobisthiazole as Weak Donor for Improved Photovoltaic Performance: Microwave Conductivity Technique Assisted Molecular Engineering

New donor–acceptor‐type copolymers comprised of benzobisthiazole (BBTz) as a weak donor rather than acceptor are proposed. This approach can simultaneously lead to deepening the HOMO and LUMO of the polymers with moderate energy offset against fullerene derivatives in bulk heterojunction organic photovoltaics. As a proof‐of‐concept, BBTz‐based random copolymers conjugated with typical electron acceptors: thienopyrroledione (TPD) and benzothiadiazole (BT) based on density functional theory calculations are synthesized. Laser‐flash and Xe‐flash time‐resolved microwave conductivity (TRMC) evaluations of polymer:[6,6]‐phenyl C₆₁ butyric acid methyl ester (PCBM) blends are conducted to screen the feasibility of the copolymers, leading to optimization of processing conditions for photovoltaic device application. According to the TMRC results, alternating BBTz‐BT copolymers are designed, exhibiting extended photoabsorption up to ca. 750 nm, deep HOMO (–5.5 to –5.7 eV), good miscibility with PCBM, and inherent crystalline nature. Moreover, the maximized PCE of 3.8%, the top‐class among BBTz‐based polymers reported so far, is realized in an inverted cell using TiO_x and MoO_x as the buffer layers. This study opens up opportunities to create low‐bandgap polymers with deep HOMO, and shows how the device‐less TRMC evaluation is of help for decision‐making on judicious molecular design.     

Identification of Fuzzy Relations with Multiple Hyperplanes by Genetic Algorithm in Structural Design

Abstract: This paper proposes a method for formulation and quantification of human subjective evaluations and uncertain numerical values by using multiple hyperplanes based on the results of questionnaires distributed to structural designers that are composed of four questions about structural design and planning, i.e., ( Q 1) structural damage , ( Q 2) structural economy in a macroscopic sense , ( Q 3) structural safety, and ( Q 4) opening patterns in facade. In this paper, some hyperplanes in multidimensional spaces are used as a method to identify fuzzy relations (states) in intelligent fuzzy networks for seismic structural planning. A genetic algorithm is employed as a search method for optimal formulations and is proved to be very effective as a method for such an identification.     

Heat capacities of NpN and AmN

The heat capacities of NpN and AmN were determined with the drop calorimetry method. The NpN and AmN samples were prepared by the carbothermic reduction of the respective dioxides. The heat capacity of NpN obtained was in good agreement with the reported values in the temperature range from 334 to 1067 K, which was close to those of UN and PuN. The heat capacity of AmN was obtained experimentally for the first time, which was slightly smaller than those of UN, NpN and PuN in the temperature range from 354 to 1071 K.     

Solution copolymerization of ethylene with α-olefins by a MgCl2 supported TiCl4 catalyst

Summary Copolymerization of ethylene with -olefins, i.e. propylene, butene-1, 4-methyl-pentene-1(4-MP-1), was carried out by a MgCl₂ supported TiCl₄ catalyst in combination with Et₃Al at a temperature as high as 170 °C at which the polymerization system was homogeneous. This catalytic system showed very a high activity and produced copolymers having a density of 0.91–0.94 g/ml. Of these three kinds of comonomers, propylene showed the highest reactivity and caused most frequently the termination of a polymer growing by chain transfer reaction and produced copolymers having the broadest MWD.     

Studies on the improvement of cured two-stage phenolics performance. III. Relation between conditions of heat treatment and properties of wood-flour-filled phenolics

The effect of heat treatment on the properties of cured two-stage phenolics was studied. Samples were compression-molded from the compound that was prepared from novolac, wood flour (100 phr), and hexamethylenetetramine (15 phr). Samples were heat-treated in conditions of four levels for temperature (150°C, 170°C, 190°C, and 210°C) and time (4, 8, 16, and 24 h). The properties of samples heat-treated, such as weight loss, dimensional stability, water absorption after boiling, and flexural properties were measured. The relation between the properties and the conditions of heat treatment was examined statistically. From the results, it was decided that the optimum conditions of heat treatment for practical use were: (i) to decrease water absorption and to heighten electrical resistance, 210°C, 24 h; (ii) to improve flexural properties at room temperature and at 160°C; 170°C, 8 h, and 170–190°C, 24 h, respectively. It was concluded that the decrease of water absorption of moldings was due to the increase of hydrophobic nature of wood flour included in moldings by heat treatment and that the improvement of flexural property of moldings at 160°C was due to an increase of crosslinking density by heat treatment. The reasons for the improvement of the electrical properties by heat treatment were also discussed.     

Studies on propylene polymerization with a highly active MgCl2 supported TiCl4 catalyst system

Summary Propylene polymerization was performed with a highly active MgCl supported TiCl₄ in conjunction with Et₃Al and ethyl benzoate (EB). The obtained polypropylene sample was separated into four fractions by successive extraction with pentane, heptane and trichloroethylene (trichlene). Yield, Mn, Tm and microtacticity of each fraction were determined, and the effects of the concentration of EB on these items of results were investigated. It has been found that EB enhances yield, Mn and stereospecificity of trichlene insoluble (the most stereospecific) fraction, and in contrast, it decreases rapidly yields of other three fractions without changing the character of the polymers. From these findings, the functions of EB to the active centers were discussed.     

In vivo evidence for non-universal usage of the codon CUG in Candida maltosa

An alkane-assimilating yeast Candida maltosa had been studied in order to establish systems suitable for biotransformation of hydrophobic compounds. However, functional expression of heterologous genes tested for this purpose had not been successful in several cases. On the other hand, it had been reported that the codon CUG, a universal leucine codon, is read as serine in C. cylindracea. The same altered codon usage had also been suggested by in vitro experiments in some Candida yeasts which are phylogenetically closely related to C. maltosa. In this study we have shown that the failure in functional expression of a heterologous gene is due to the fact that the codon CUG is read as serine in C. maltosa. This conclusion was drawn from the following experimental results: (1) when a cytochrome P450 gene of C. maltosa containing a CTG codon was expressed in C. maltosa, the corresponding amino acid was found to be serine, and not leucine; (2) a tRNA gene with an almost identical structure to that of the tRNA ^SerCAG gene of C. albicans could be isolated from the genome of C. maltosa; (3) the Saccharomyces cerevisiae URA3 gene, which has one CTG codon, could not complement the ura3 mutation of C. maltosa as itself, but when the CTG codon was changed to another leucine codon, CTC, the mutated gene could complement the ura3 mutation. The last result is the first example of succeeding in functional expression of a heterologous gene in Candida species having an altered codon usage by changing the CTG codon in the gene to another codon. The nucleotide sequence datum reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with the Accession Number D26074.     

Modularization and abstraction in logic programming

In knowledge information processing, the structuring of knowledge and algorithms is one of the key issues. The goal of this work is to introduce the concepts and mechanisms of abstraction, modularization and parameterization into logic programming, which is one of the preliminary steps toward creating a kernel language for fifth generation computer systems.     

Contrasting diurnal variations in fossil and nonfossil secondary organic aerosol in urban outflow, Japan

Diurnal variations of fossil secondary organic carbon (SOC) and nonfossil SOC were determined for the first time using a combination of several carbonaceous aerosol measurement techniques, including radiocarbon (1?C) determinations by accelerator mass spectrometry, and a receptor model (chemical mass balance, CMB) at a site downwind of Tokyo during the summer of 2007. Fossil SOC showed distinct diurnal variation with a maximum during daytime, whereas diurnal variation of nonfossil SOC was relatively small. This behavior was reproduced by a chemical transport model (CTM). However, the CTM underestimated the concentration of anthropogenic secondary organic aerosol (ASOA) by a factor of 4-7, suggesting that ASOA enhancement during daytime is not explained by production from volatile organic compounds that are traditionally considered major ASOA precursors. This result suggests that unidentified semivolatile organic compounds or multiphase chemistry may contribute largely to ASOA production. As our knowledge of production pathways of secondary organic aerosol (SOA) is still limited, diurnal variations of fossil and nonfossil SOC in our estimate give an important experimental constraint for future development of SOA models.