Roles of K151 and D180 in L‐2‐haloacid dehalogenase from Pseudomonas sp. YL: Analysis by molecular dynamics and ab initio fragment molecular orbital calculations

L ‐2‐haloacid dehalogenase (L ‐DEX) catalyzes the hydrolytic dehalogenation of L ‐2‐haloalkanoic acids to produce the corresponding D ‐2‐hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L ‐DEX from Pseudomonas sp. YL (L ‐DEX YL) by using molecular modeling. The complexes of wild‐type L ‐DEX YL and its K151A and D180A mutants with its typical substrate, L ‐2‐chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6‐31G level to estimate interfragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L ‐2‐chloropropionate, catalytic water, nucleophile (D10), and with each other. Our calculations suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while D180 stabilizes the rotation of the nucleophile D10, fixes catalytic water around D10, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L ‐DEX YL with improved enzymatic activity or substrate specificity. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

On the existence of multiple positive solutions of quasilinear elliptic eigenvalue problems

We study a quasilinear elliptic problem

Redox-responsive conformational alteration of aromatic amides bearing N-quinonyl system

Redox-induced conformational alteration of N-aryl-N-phenylamides, in which the N-aryl group consists of a hydroquinone–p-quinone system, was examined. The reduced form bearing a dihydroxyphenyl or dimethoxyphenyl group exists mainly in the E-form, whereas the oxidized form bearing a N-benzoquinone moiety takes the Z-form both in the crystal and in solution. This redox-induced conformational alteration is associated with a marked change in optical properties. This system appears to have suitable properties for use in external redox stimulus-responsive functional switching.     

A practical ortho-rearrangement of silyl group of ortho-bromophenyl silyl ethers using magnesium(0)

A practical synthesis of ortho-silyl-substituted phenol from ortho-bromophenyl silyl ethers without using RLi is described. Various ortho-bromophenyl silyl ethers are treated with commercially available Mg turnings, which are easy to handle in air, and transfer of the silyl group to the ortho-position occurs in good to high yields. Selective mono-magnesiation of 2,6-dibromophenyl silyl ether is observed even in the presence of excess Mg, and ortho-bromo-6-silylphenol is obtained as the predominant product. The obtained ortho-silyl-substituted phenol is formylated with (CH₂O)_n/MgCl₂/Et₃N, and then condensation with a diamine leads to a silyl-substituted salen-type ligand in a good yield. This scheme is suitable for the large scale synthesis of silyl-substituted salen-type ligands bearing imine groups.     

Plateaus in the dispersion of two-dimensional magnetoplasmons in GaAs quantum wells: theoretical evidence of an electron reservoir

The filling-factor-dependent plateau-type dispersion of the long-wavelength magnetoplasmon in high-mobility two-dimensional electron system observed by Holland et al. [Phys. Rev. Lett. 93, 186804 (2004)10.1103/PhysRevLett.93.186804] can be explained by the well-established semiclassical dispersion, by adopting the electron reservoir hypothesis previously proposed in order to explain the integer quantum Hall effects.     

Accelerating cosmologies from spacelike branes

We point out that the recently proposed model of a flat four-dimensional universe with accelerated expansion in string or M theory is a special case of time-dependent solutions that the author found under the name of spacelike (S) branes. We also show that similar accelerating models can be obtained from S branes if the internal space is chosen to be hyperbolic or flat spaces.     

Analytic hierarchy based policy design method (AHPo) for solving societal problems that require a multifaceted approach

This paper proposes an AHP based statistical method for the design of a comprehensive policy alternative, AHPo, for solving societal problems that require a multifaceted approach. In the proposed method, criteria relevant to the goal or focus are structured in the same way as in the conventional AHP. However, these two methods are quite different in regard to the method of quantification. The new method predicts or analyses the impact of the policy alternatives on the overall goal. In other words, it predicts or rationalizes the way people appreciate the situation in which an alternative is adopted and implemented. It will serve as a tool for supporting (especially political) decision making.     

Oscillation theory of first order functional differential equations with deviating arguments

Summary New oscillation criteria are established for the first order functional differential equation (*) y'(t)+p(t)y(g(t))=0and its nonlinear analogue. The results are presented so that a remarkable duality existing between the case where (*) is retarded (g(t)t) is apparent. Possible extension of the results for (*) to equations with several deviating arguments is attempted. Finally, it is shown that there exists a class of autonomous equations for which the oscillation situation can be completely characterized.     

Creation of magnetic cerasomes through electroless plating and their manipulation using external magnetic fields

Magnetic cerasome, an artificial cell membrane having ultrathin magnetic metal layers on the surface, was prepared through electroless plating of magnetic metal alloy onto an organic–inorganic vesicular nanohybrid “cerasome.” Morphological and functional characteristics of the magnetic cerasome were evaluated using various physical measurements: scanning and transmission electron microscopies, energy-dispersive X-ray spectroscopy, electron tomography, and vibrating sample magnetometry. The results proved that high morphological stability of the cerasome was important for constructing the magnetic lipid vesicle and that insertion of an alkylated metal ligand into the cerasome was essential to the magnetic metal alloy deposition on the cerasome surface. Fluorescence microscopic observations revealed that the magnetic cerasomes were collected reversibly on the slide glass surface and manipulated depending on external motion of a magnet. The potential use of the magnetic cerasomes as a novel vesicular nanohybrid is also described in this report.     

Thermal behavior of perlite concrete used in a sodium-cooled fast reactor

Journal of Thermal Analysis and Calorimetry - In this study, the thermal behavior of the perlite concrete used in a sodium-cooled fast reactor was investigated for obtaining information on a plant...