The Spherical Expansion of H2 Dimer Interaction Energy by Double Symmetry-Adapted Perturbation Theory

Abstract

The weak interaction energy of H₂ dimer is studied by double symmetry-adapted perturbation theory (SAPT) within second-order of intermolecular and intramonomer perturbation for molecular simulations. The assumed orientations of H₂ dimer are linear, parallel, T type and X type. Among four orientations T orientation is the most stable, while linear orientation is the most repulsive. The second-order dispersion energy E _disp ⁽²⁾ is the most attractive contribution in all orientations. The interaction energy has the anisotropy, so we expressed our total interaction energy by the spherical expansion to compare with the experimental value. The isotropic interaction energy is about 85% of the experimental value.     

Conformational restriction approach to BACE1 inhibitors II: SAR study of the isocytosine derivatives fixed with a cis-cyclopropane ring

To improve the efficacy of the conformationally restricted BACE1 inhibitors, structural modifications were investigated using two strategies: (a) modification of the terminal aromatic ring and (b) insertion of a spacer between the aromatic rings. In the latter approach, another type of inhibitor 17 bearing an ethylene spacer between two aromatic rings was found to exhibit good BACE1 inhibitory activity, while the corresponding conformationally unrestricted compound 25 showed no activity. This result revealed an interesting effect of a conformational restriction with a cyclopropane ring.     

Occurrence of 4-tert-butylphenol (4-t-BP) biodegradation in an aquatic sample caused by the presence of Spirodela polyrrhiza and isolation of a 4-t-BP-utilizing bacterium

Although 4-tert-butylphenol (4-t-BP) is a serious aquatic pollutant, its biodegradation in aquatic environments has not been well documented. In this study, 4-t-BP was obviously and repeatedly removed from water from four different environments in the presence of Spirodela polyrrhiza, giant duckweed, but 4-t-BP persisted in the environmental waters in the absence of S. polyrrhiza. Also, 4-t-BP was not removed from autoclaved pond water with sterilized S. polyrrhiza. These results suggest that the 4-t-BP removal from the environmental waters was caused by biodegradation stimulated by the presence of S. polyrrhiza rather than by uptake by the plant. Moreover, Sphingobium fuliginis OMI capable of utilizing 4-t-BP as a sole carbon and energy source was isolated from the S. polyrrhiza rhizosphere. Strain OMI degraded 4-t-BP via a meta-cleavage pathway, and also degraded a broad range of alkylphenols with linear or branched alkyl side chains containing two to nine carbon atoms. Root exudates of S. polyrrhiza stimulated 4-t-BP degradation and cell growth of strain OMI. Thus, the stimulating effects of S. polyrrhiza root exudates on 4-t-BP-degrading bacteria might have contributed to 4-t-BP removal in the environmental waters with S. polyrrhiza. These results demonstrate that the S. polyrrhiza–bacteria association may be applicable to the removal of highly persistent 4-t-BP from wastewaters or polluted aquatic environments.     

Possible molecular evolution of biomembranes: from single-chain to double-chain lipids

We have studied a possible evolution process permitting a 'primitive' membrane to evolve towards a membrane structure with an outer wall, similar to that of bacteria. We have investigated whether a polysaccharide bearing hydrophobic phytyl or cholesteryl chains coats giant vesicles made of single- or double-chain lipids. Phytyl-pullulan 5b was found to bind to the surface of vesicles made of either single- or double-chain lipids. In contrast, cholesteryl-pullulan 5a only coated the surface of vesicles made of double-chain lipids. These results indicate that there must be a close match between the size and shape of membrane constituents and the hydrophobic molecules to be inserted. This process could, thus, provide a selection mechanism of lipid-membrane constituents during the course of biomembrane evolution. The presence of the above 'hydrophobized' polysaccharides on the surface of different giant vesicles was identified by lectin binding. Both concanavalin A and annexin V were shown by fluorescence microscopy to bind spontaneously to vesicles made of double-chain lipids. Our experiments exemplify that self-organization of amphiphiles into closed vesicles in aqueous solution automatically leads to the coating of vesicles by 'hydrophobized' polysaccharides, which then permit lectin binding. This is a possible mechanism for the evolution of primitive membranes towards 'proto-cells'.     

Primary structure and expression of a 24-kD vacuolar protein (VP24) precursor in anthocyanin-producing cells of sweet potato in suspension culture

A 24-kD vacuolar protein (VP24) accumulates abundantly in intravacuolar pigmented globules in anthocyanin-containing sweet potato (Ipomoea batatas) cells in suspension culture. A cDNA clone encoding VP24 was isolated from a cDNA library constructed from light-irradiated suspension-cultured cells. Sequence analysis revealed that a 2.9-kbp VP24 cDNA encodes a protein of 893 amino acid residues with a molecular mass of 96.3 kD. According to the deduced amino acid sequence of VP24 cDNA, VP24 is probably synthesized as a large precursor protein with an N-terminal extension composed of a signal peptide and a propeptide, plus the polypeptide of the mature VP24 and its C-terminal propeptide, which contains the multiple transmembrane domains. A search in the ProDom database revealed the mature VP24 domain belongs to the zinc metalloprotease family. Northern analysis revealed that the single 2.9-kb VP24 mRNA increases rapidly after light irradiation, whereas VP24 mRNA was undetectable in the dark-cultured cells or in the presence of a high concentration of 2,4-dichlorophenoxyacetic acid. Light-induced VP24 gene expression closely correlated with the accumulation of anthocyanin in the vacuoles. These results suggested that proteins derived from the VP24 precursor protein may be involved in vacuolar transport and/or accumulation of anthocyanin synthesized in the cytosol.     

Molecular Orbital Study of the Magnetic Properties of Pyrazine- and Pyrimidine-Bridged Copper(II) Complexes

Magnetic interactions in the three copper(II)-complex polymers, [Cu(PZ)(NO₃)₂]_n, [Cu(PM)(NO₃)₂(H₂O)₂]_n, and [Cu(PM)₂(NO₃)₂]_n are discussed on the basis of extended Hückel calculations inthe formulas PZ and PM stand for pyrazine and pyrimidine, respectively. Interactions between the Cu-3d orbitals and the lone-pair orbitals of pyrazine and pyrimidine are analyzed from the viewpoint of `through-space' and `through-bond' interactions using binuclear complexes to model the three copper(II) polymers. Three conclusions can be drawn from the orbital interaction analysis: (1) in the first polymer, a superexchange pathway is formed with the bond of Cu–-N and the through-bond interaction between the lone pairs of the nitrogen atoms of pyrazine will lead to an antiferromagnet state; (2) in the second polymer a superexchange pathway is formed with the bond of Cu–-N and the through-space interaction between the lone pairs of the nitrogen atoms of pyrimidine, and as a result an antiferromagnetic state will be preferred; and (3) in the third polymer., there is no effective pathway in respect of overlap interaction and the HOMO and the LUMO are actually degenerate, and thus a ferromagnetic state will arise. The band structures are analyzed to characterize the magnetic properties of the antiferromagnetic polymers, [Cu(PZ)(NO₃)₂]_n and [Cu(PM)(NO₃)₂(H₂O)₂], and the ferromagnetic polymer, [Cu(PM)₂(NO₃)₂]_n.     

Effects on RNAi of the tight structure, sequence and position of the targeted region

RNA interference (RNAi) is a gene-silencing phenomenon that involves the double-stranded RNA-mediated cleavage of mRNA, and small interfering RNAs (siRNAs) can cause RNAi in mammalian cells. There have been many attempts to clarify the mechanism of RNAi, but information about the relationship between the sequence and structure, in particular, a tight structure, of the target RNA and the activities of siRNAs are limited. In the present study, we examined this relationship by introducing the TAR element, which adopts a very stable secondary structure, at different positions within target RNAs. Our results suggested that the activities of siRNAs were affected by the tight stem–loop structure of TAR. In contrast, the position of the target within the mRNA, the binding of the Tat protein to the TAR, and the location of the target within a translated or a noncoding region had only marginal effects on RNAi. When the target sequence was placed in two different orientations, only one orientation had a significant effect on the activities of siRNA, demonstrating that the presence of certain nucleotides at some specific positions was favorable for RNAi. Systematic analysis of 47 different sites within 47 plasmids under identical conditions indicated that it is the target sequence itself, rather than its location, that is the major determinant of siRNA activity.     

DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil

A denaturing gradient gel electrophoresis (DGGE) method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil is presented. Five specific primers for 16S rDNA of methanogenic archaea, which were modified from the primers for archaea, were first evaluated by polymerase chain reaction and DGGE using genomic DNAs of 13 pure culture strains of methanogenic archaea. The DGGE analysis was possible with two primer pairs (0348aF-GC and 0691R; 0357F-GC and 0691R) of the five pairs tested although 16S rDNA of some non-methanogenic archaea was amplified with 0348aF-GC and 0691R. These two primer pairs were further evaluated for use in analysis of methanogenic archaeal community in Japanese paddy field soil. Good separation and quality of patterns were obtained in DGGE analysis with both primer pairs. A total of 41 DNA fragments were excised from the DGGE gels and their sequences were determined. All fragments belonged to methanogenic archaea. These results indicate that the procedure of DGGE analysis with the primer pair 0357F-GC and 0691R is suitable for investigating methanogenic archaeal community in paddy field soil.