Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Optimized conditions for high-performance liquid chromatography analysis of oligosaccharides using 7-amino-4-methylcoumarin as a reductive amination reagent

Reductive amination reaction using 7-amino-4-methylcoumarin (AMC) as a fluorescent probe enabled analyses of glycoproteins' monosaccharides and N-linked oligosaccharides. Reductive amination of N-acetylhexosamines and AMC using sodium cyanoborohydride or dimethylamine-borane complex indicated slight recovery of derivatives, but pyridine-borane achieved better recoveries. Reversed-phase high-performance liquid chromatography (HPLC) analyses of monosaccharides constituting glycoprotein glycans using fluorimetric detection revealed linearity for 0.2fmol to 1pmol, with less than 5% RSD quantitation reproducibility. Reversed-phase HPLC analyses of glycoprotein glycans, combined with negative-ion electrospray ionization mass spectrometry (LC-ESI-MS), enabled their structural determination. Using this highly hydrophobic reagent, AMC-labeled oligosaccharides displayed one-order to two-order higher ESI-MS intensity than derivatives labeled using other reagents.     

Sequence-specifically platinum metal deposition on enzymatically synthesized DNA block copolymer

Platinum metal was sequence-specifically deposited on the DNA block copolymer synthesized by the Klenow fragment of E. coli DNA polymerase I (3'-5' exonuclease deficient).     

Sequence-specific control of azobenzene assemblies by molecular recognition of DNA

We investigated the molecular recognition between the amphiphile AzoAde, which is composed of azobenzene in the hydrophobic and adenine in the hydrophilic portion of the molecule, and oligonucleotides having a homogeneous base (dA30, dT30, dG30, and dC30) at the air-water interface. On the basis of the complementary base-pairing of DNA in the duplex, orderly arrangement of AzoAde on templated dT30 was examined using pi-A isotherm, UV-vis RAS, FT-IR RAS, and XPS measurements. Although there was little interaction between AzoAde and mismatched oligonucleotides (dA30, dG30, and dC30), AzoAde prepared on a dT30 subphase stoichiometrically assembled and interacted with dT30, subsequently forming a J-form assembly at the air-water interface. AFM observation of the LB films revealed the nanostructure of the J-formed AzoAde monolayer on the dT30 subphase as well as the domain structures of the H-formed monolayers on the other oligonucleotide subphases. Therefore, dT30 has a potential application as a template for assembling AzoAde at the air-water interface.     

Reduced hydrophobic interaction of polystyrene surfaces by spontaneous segregation of block copolymers with oligo (ethylene glycol) methyl ether methacrylate blocks: force measurements in water using atomic force microscope with hydrophobic probes

Reduction of hydrophobic interaction in water is important in biological interfaces. In our previous work, we have found that poly(styrene- b-triethylene glycol methyl ether methacrylate) (PS-PME3MA) segregates the PME3MA block to the surface in hydrophobic environment, such as in air or in a vacuum, and shows remarkable resistance against adsorption or adhesion of proteins, platelets, and cells in water. In this paper, we report that atomic force microscopy (AFM) with hydrophobic probes can directly monitor the reduced hydrophobic interaction of the PS surfaces modified by poly(styrene- b-origoethylene glycol methyl ether methacrylate) (PS-PME NMA), where N is the number of ethylene glycol units. The pull-off forces between the hydrophobic probes that are coated with octyltrichlorosilane (OLTS) and the PS-PME NMA modified polystyrene (PS) surfaces in water were measured. The absolute spring constants and tip-curvatures of the AFM cantilevers were measured to compute the work of adhesion by the Johnson, Kendall, and Roberts (JKR) theory, which relates the pull-off force at which the separation occurs between a hemisphere and a plane to the work of adhesion. The hydrophobic interactions between the hydrophobic tip and polymer surfaces in water were greatly reduced with the segregated PME NMA blocks. The hydrophobic interactions decrease with increasing N of the series of PS-PME NMA and show a correlation with the amount of protein adsorbed.     

Module assembly for protein-surface recognition: geranylgeranyltransferase I bivalent inhibitors for simultaneous targeting of interior and exterior protein surfaces

Synthetic chemical probes designed to simultaneously targeting multiple sites of protein surfaces are of interest owing to their potential application as site specific modulators of protein-protein interactions. A new approach toward bivalent inhibitors of mammalian type I geranylgeranyltransferase (GGTase I) based on module assembly for simultaneous recognition of both interior and exterior protein surfaces is reported. The inhibitors synthesized in this study consist of two modules linked by an alkyl spacer; one is the tetrapeptide CVIL module for binding to the interior protein surface (active pocket) and the other is a 3,4,5-alkoxy substituted benzoyl motif that contains three aminoalkyl groups designed to bind to the negatively charged protein exterior surface near the active site. The compounds were screened by two distinct enzyme inhibition assays based on fluorescence spectroscopy and incorporation of a [(3)H]-labeled prenyl group onto a protein substrate. The bivalent inhibitors block GGTase I enzymatic activity with K(i) values in the submicromolar range and are approximately one order of magnitude and more than 150 times more effective than the tetrapeptide CVIL and the methyl benzoate derivatives, respectively. The bivalent compounds 6 and 8 were shown to be competitive inhibitors, suggesting that the CVIL module anchors the whole molecule to the GGTase I active site and delivers the other module to the targeting protein surface. Thus, our module-assembly approach resulted in simultaneous multiple-site recognition, and as a consequence, synergetic inhibition of GGTase I activity, thereby providing a new approach in designing protein-surface-directed inhibitors for targeting protein-protein interactions.     

Polymer-like polyphenols of black tea and their lipase and amylase inhibitory activities

Lipase and amylase inhibitory activities of black tea were examined. After solvent partitioning of a black tea extract with the ethyl acetate and n-butanol, the two soluble fractions showed comparable inhibitory activities. Activity in the ethyl acetate fraction was mainly attributable to polyphenols with low-molecular weights, such as theaflavin gallates. On the other hand, the active substance in the n-butanol layer was ascertained to be a polymer-like substance. 1H- and 13C-NMR spectra showed signals arising from the flavan A-ring and galloyl groups, although signals due to flavan B-rings were not detected, suggesting that the polymer-like substances were generated by oxidative condensation of flavan B-rings, a result which was previously deduced from our results of in vitro catechin oxidation experiments. Enzymatic oxidation of epicatechin 3-O-gallate produced a similar polymer-like substance and suggested that condensation between a B-ring and galloyl groups was involved in the polymerization reaction.     

Iron speciation and mineral characterization of upper Jurassic reservoir rocks in the Minhe Basin,NW China

Six samples from a natural outcrop of reservoir rocks with oil seepage and two control samples from surrounding area in the Minhe Basin, northwestern China were selectively collected and analyzed for mineralogical composition as well as iron speciation using X-ray powder diffraction (XRD) and Mössbauer spectroscopy, respectively. Iron species revealed that: (1) the oil-bearing reservoir rocks were changed by water-rock-oil interactions; (2) even in the same site, there was a different performance between sandstone and mudstone during the oil and gas infusion to the reservoirs; and (3) this was evidence indicating the selective channels of hydrocarbon migration. In addition, these studies showed that the iron speciation by Mössbauer spectroscopy could be useful for the study of oil and gas reservoirs, especially the processes of the water-rock interactions within petroleum reservoirs.