Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis

Cytochrome P450 (CYP) is deeply involved in the metabolism of chemicals including pharmaceuticals. Therefore, polymorphisms of this enzyme have been widely studied to avoid unfavorable side effects of drugs in chemotherapy. In this work, we performed computational analysis of the mechanism of the decrease in enzymatic activity for three typical polymorphisms in CYP 2C9 species: *2, *3, and *5. Based on the equilibrated structure obtained by molecular dynamics simulation, the volume of the binding pocket and the fluctuation of amino residues responsible for substrate holding were compared between the wild type and the three variants. Further docking simulation was carried out to evaluate the appropriateness of the binding pocket to accommodate substrate chemicals. Every polymorphic variant was suggested to be inferior to the wild type in enzymatic ability from the structural viewpoint. F‐G helices were obviously displaced outward in CYP2C9*2. Expansion of the binding pocket, especially the space near F′ helix, was remarkable in CYP2C9*3. Disappearance of the hydrogen bond between K helix and β4 loop was observed in CYP2C9*5. The reduction of catalytic activity of those variants can be explained from the deformation of the binding pocket and the consequent change in binding mode of substrate chemicals. The computational approach is effective for predicting the enzymatic activity of polymorphic variants of CYP. This prediction will be helpful for advanced drug design because calculations forecast unexpected change in drug efficacy for individuals. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Acceptable range of speech level in noisy sound fields for young adults and elderly persons

The acceptable range of speech level as a function of background noise level was investigated on the basis of word intelligibility scores and listening difficulty ratings. In the present study, the acceptable range is defined as the range that maximizes word intelligibility scores and simultaneously does not cause a significant increase in listening difficulty ratings from the minimum ratings. Listening tests with young adult and elderly listeners demonstrated the following. (1) The acceptable range of speech level for elderly listeners overlapped that for young listeners. (2) The lower limit of the acceptable speech level for both young and elderly listeners was 65 dB (A-weighted) for noise levels of 40 and 45 dB (A-weighted), a level with a speech-to-noise ratio of +15 dB for noise levels of 50 and 55 dB, and a level with a speech-to-noise ratio of +10 dB for noise levels from 60 to 70 dB. (3) The upper limit of the acceptable speech level for both young and elderly listeners was 80 dB for noise levels from 40 to 55 dB and 85 dB or above for noise levels from 55 to 70 dB.     

Diagonal composite order in a two-channel Kondo lattice

A novel type of symmetry breaking is reported for the two-channel Kondo lattice where conduction electrons have spin and orbital (channel) degrees of freedom. Using the continuous-time quantum Monte?Carlo and the dynamical mean-field theory, a spontaneous breaking of the orbital symmetry is observed. The tiny breakdown of orbital occupation number, however, vanishes if the conduction electrons have the particle-hole symmetry. The proper order parameter instead is identified as a composite quantity representing the orbital-selective Kondo effect. The single-particle spectrum of the selected orbital shows insulating property, while the other orbital behaves as a Fermi liquid. This composite order is the first example of odd-frequency order other than off-diagonal order (superconductivity), and is a candidate of hidden order in f-electron systems.     

Light focusing by slot Fabry-Perot photonic crystal nanoresonator on scanning tip

We numerically investigate the propagation of light through the photonic crystal (PhC) waveguide on low refraction index material for near-field light focusing at the visible wavelength (635 nm) by incorporating a center air slot and Fabry-Perot resonator on the scanning tip. Perturbations by water and substrate refraction index changes of the PhC are analyzed by the finite-difference time-domain method to show minimal impact on light confinement and throughput. Such a total dielectric probe tip design has great potential to complement the current widely used metal-coated optical-fiber-based light confinement probe.     

Control of mixed protonic and electronic conductivity by mixing rare-earth ortho-borates

In order to develop mixed protonic and electronic conductors, we proposed a novel concept for material design that enables to control partial conductivities by fabricating solid solutions of protonic and electronic conductors. In this work, Sr-doped LaBO₃ and Sr-doped CeBO₃ were chosen as model compounds conducting protons and electron holes, respectively. Solid solutions of the above borates, Sr-doped La_1 − xCe_xBO₃, were prepared, and their electrical conductivities were investigated in 8.5 × 10²-4.2 × 10³ Pa of p(H₂O) and 1.0 × 10-1.0 × 10⁵ Pa of p(H₂) at 1073 K. From the experimental results of the gas partial pressure dependences of the conductivities, major charge carrier species were identified as a function of x. It was found that proton was the major charge carrier when x < 0.2 while the contribution of the electron hole conduction became remarkable as x increased above 0.2. The contribution of the electron hole conduction can be interpreted by the percolation model.     

Salt‐Free Reduction of Nonprecious Transition‐Metal Compounds: Generation of Amorphous Ni Nanoparticles for Catalytic C–C Bond Formation

A salt‐free procedure for the generation of a wide variety of metal(0) particles, including Fe, Co, Ni, and Cu, was achieved using 2,3,5,6‐tetramethyl‐1,4‐bis(trimethylsilyl)‐1,4‐diaza‐2,5‐cyclohexadiene ( 1 ), which reduced the corresponding metal precursors under mild conditions. Notably, Ni particles formed in situ from the treatment of Ni(acac)₂ (acac=acetylacetonate) with 1 in toluene exhibited significant catalytic activity for reductive C? C bond‐forming reactions of aryl halides in the presence of excess amounts of 1 . By examination of high‐magnification transmission electron microscopy images and electron diffraction patterns, we concluded that amorphous Ni nanoparticles (Ni aNPs) were essential for the high catalytic activity.     

2,2′-Bipyridyl formation from 2-arylpyridines through bimetallic diyttrium intermediate

An alkylyttrium complex supported by an N,N′-bis(2,6-diisopropylphenyl)ethylenediamido ligand, (ArNCH₂CH₂NAr)Y(CH₂SiMe₃)(THF)₂ (1, Ar = 2,6-ⁱPr₂C₆H₃), activated an ortho-phenyl C–H bond of 2-phenylpyridine (2a) to form a (2-pyridylphenyl)yttrium complex (3a) containing a five-membered metallacycle. Subsequently, a unique C(sp²)–C(sp²) coupling of 2-phenylpyridine proceeded through a bimetallic yttrium intermediate, derived from an intramolecular shift of the yttrium center to an ortho-position of the pyridine ring in 3a, to yield a bimetallic yttrium complex (4a) bridged by two-electron reduced 6,6′-diphenyl-2,2′-bipyridyl. Aryl substituents at the ortho-position of the pyridine ring were key in order to destabilize the μ,κ²-(C,N)-pyridyldiyttrium intermediate prior to the C(sp²)–C(sp²) bond formation.