Theoretical prediction of optical absorption maxima for photosensory receptor mutants

We found a linear correlation between the theoretically predicted shifts and experimentally observed absorption spectra for various mutants of photoactive yellow protein, a photosensory receptor. Excitation energies of mutants were evaluated by the combination of the high level ab initio calculation for the chromophore inside and the low level ab initio calculation for the surrounding protein environment. Importantly, the electronic states of these two regions were treated both as variables and they are solved consistently to each other. The protein–chromophore interaction has been accurately reproduced by this method.     

Monocyclic rod-type liquid crystals; 2,5-dialkanoyloxytropones and 5-alkanoyloxy-2-alkoxytropones

Two kinds of monocyclic troponoid mesogens, 2,5-dialkanoyloxytropones (4) and 5-alkanoyloxy2-alkoxytropones (5), were prepared. The former showed monotropic smectic A phases and the virtual isotropic liquid-smectic A transitions of the latter were determined by extrapolation of results in a binary phase diagram. Comparing the mesogenic properties between the tropones 4 and the 2-alkanoyloxy-5-alkoxytropones (1), the alkanoyloxy group at C-5 enhances both the melting points and the transition temperatures of the smectic A phases. From the comparison between 5 and 1, the alkanoyloxy group at C-2 lowers the melting points.     

Control of a class of underactuated mechanical systems

In this paper a new control methodology for underactuated mechanical systems is proposed. The basic idea of this method is to combine passive velocity field control with decoupling vector field. In order that the underactuated mechanical systems can be stabilized at the desired position after settling on the desired velocity vector field, novel control strategies are proposed. Proposed control strategies are applied to the underactuated planar three-link manipulator and underactuated planar body. Simulations demonstrate the usefulness and effectiveness of the proposed control methodology.     

Prediction of carcinogenicity of polynuclear aromatic hydrocarbons on the basis of their chemical structures

The carcinogenicities of polynuclear aromatic hydrocarbons in particulates extracted from diesel engine exhaust are predicted on the basis of the combined bay-L region theory proposed earlier, in conjunction with pattern recognition techniques. The predicted carcinogenicities agree well with experimental data, thus showing the validity of the proposed model equations.     

A Mössbauer spectroscopy study on iron in marine sediments

The chemical states of iron in near-shore and deep-sea sediments were investigated by means of⁵⁷Fe Mössbauer spectroscopy using selective and chemical leachings. The Fe²⁺/Fe³⁺ ratios of deep-sea sediments were much smaller than those of near-shore sediments, while the total contents of iron in the former were much higher than those in the latter. This is principally due to the high content of hydrogenous ferric oxyhydroxide in deep-sea sediments. Also, in the aluminosilicate fraction, the Fe²⁺/Fe³⁺ ratios of deep-sea sediments were smaller than those of near-shore sediments. This is probably attributed to the difference in the silicate mineral composition between deep-sea and near-shore sediments. X-ray reflections of clay minerals normalized to those of feldspars and quartz were more intense in deep-sea sediments than in near-shore sediments.     

Modulated Microdomain Switching of Nematic Liquid Crystals

Abstract

Modulated microdomain switching of nematic liquid crystals have been investigated. This display mode used for light switching of micron-sized domains regions using a complicated electric field with special mesh electrode structures. Under He-Ne laser irradiation, contrast ratio was 22:1 for homeotropic alignment cell and transmittance change was no dependent of incident polarization condition. Under white light illumination, the contrast ratio was 4.3:1.     

Reactivity of halophenol and formation of phenoxo–copper(II) complex in basic copper-catalyzed halogen displacement polymerization

The halogen displacement polymerization of 2,4,6-trihalophenol with heterogeneous basic copper(II) complex is described. The corresponding poly(dihalophenylene oxides) have been obtained from 2,4,6-trichloro-, 2,4,6-tribromo-, and 2,4,6-triiodophenol with the present catalytic system. In the halophenols used, the order of reactivity was as follows; 2,4,6-trichloro- < 2,4,6-tribromo- < 2,4,6-triiodophenol. With 2,4,6-trichlorophenol as a monomer, the 2,4,6-trichlorophenoxo–copper(II) complex, which had the composition Cu(OCH₃)(C₆H₂Cl₃O) and was considered to be a reaction intermediate, was isolated. The ESR spectrum of this complex at room temperature showed a sharp peak considered to be free organic radical, in addition to the broad one based on copper(II) ion. Poly(dichlorophenylene oxide) was obtained by thermal decomposition of the phenoxo–copper(II) complex. It was concluded that the formation and decomposition of the phenoxo–copper(II) complex were intermediate steps of halogen displacement polymerization of 2,4,6-trihalogenophenol with heterogeneous basic copper(II) catalyst.     

Theoretical study of conformational transition of CDK4 by association of cyclin D3

ABSTRACT

We present coarse-grained simulations to investigate folding and association of cyclin-dependent kinase 4 (CDK4) with cyclin D3. In our simulations, the Gō-like model and our coarse-grained model are applied to describe intramolecular and intermolecular interaction of protein molecules, respectively. We investigate conformational stability of each state of CDK4 with/without association to cyclin D3 on a single basin potential with reference to each state of CDK4. The results of simulations for the native CDK4 with cyclin D3 are consistent with an experimental observation. The open CDK4 may associate to cyclin D3 on a different interface from cyclin D3-native CDK4 complex structure. If the open CDK4 associates to cyclin D3, the open CDK4 can slightly fold and become smaller, suggesting an unfolded intermediate. After a double-basin potential with reference to the native and open states of CDK4 is given, the open CDK4 associated with cyclin D3 can smoothly shift to the native CDK4. We propose a structure of a potential candidate of an unfolded intermediate during activation of CDK4.     

Antigen�Cantibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

Effective interactions between amino acid residues in antigen?Cantibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller?CPlesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C_?? site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.