Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method

The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian 2-3 to human 2-6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics.     

Ferromagnetic fluctuation and possible triplet superconductivity in NaxCoO2.yH2O: fluctuation-exchange study of the multiorbital Hubbard model

Spin and charge fluctuations and superconductivity in NaxCoO2.yH(2)O are studied based on a multiorbital Hubbard model. Tight-binding parameters are determined to reproduce the results of band calculations. By applying the fluctuation-exchange approximation, we show that the Hund's-rule coupling between the Co t(2g) orbitals causes ferromagnetic (FM) spin fluctuation. Triplet fy((y(2)-3x(2)))-wave and p-wave pairings are favored by this FM fluctuation on the hole-pocket band. We propose that, in NaxCoO2.yH(2)O, the Co t(2g) orbitals and interorbital Hund's-rule coupling play important roles on the triplet pairing, and this compound can be a first example of the triplet superconductor in which the orbital degrees of freedom play substantial roles.     

Flow-injection analysis of silicate rocks for total iron and aluminium

A flow-injection method is described for the spectrophotometric determination of total iron and aluminium in silicate rocks. Rock samples are opened up by fusion with a mixture of lithium carbonate and boric acid, the melt is taken up in 1M hydrochloric acid and the resulting solution is used for the determination of both iron and aluminium. The flow system for the determination of iron needs no particular reagents, involving simply measurement of the absorbance of the chloro-complex of iron(III) at 335 nm. The system for aluminium consists of the reduction of iron(III) to iron(II), colour development with Xylenol Orange (XO), destruction of XO-chelates other than that of aluminium by addition of EDTA and subsequent measurement of the absorbance of the aluminium-XO complex at 506 nm. The systems permit semi-automatic, rapid analysis of silicate rocks for iron and aluminium. Results obtained for standard rocks were in good agreement with the recommended values. The precision ranged from 0.1 to 0.9% for iron and from 0.3 to 0.7% for aluminium.     

Relative quantification of enantiomers of chiral amines by high-throughput LC–ESI-MS/MS using isotopic variants of light and heavy l-pyroglutamic acids as the derivatization reagents

l-Pyroglutamic acid (l-PGA) was evaluated as a chiral labeling reagent for the enantioseparation of chiral amines in terms of separation efficiency by reversed-phase chromatography and detection sensitivity by ESI-MS/MS. Several amines and amino acid methyl esters were used as typical representatives of the chiral amines. Both enantiomers of the chiral amines were easily labeled with l-PGAs at room temperature for 60 min in the presence of 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide and 1-hydroxy-1H-benzotriazole as the activation reagents. The resulting diastereomers were completely separated by reversed-phase chromatography using the small particle (1.7 μm) ODS column (Rs = 1.6–6.8). A highly sensitive detection at a low-fmol level (1–4 fmol) was also obtained from the multiple reaction monitoring (MRM) chromatograms. Therefore, a high-throughput determination was achieved by the present UPLC–ESI-MS/MS method.     

Synthesis and properties of 2-azidodeoxyadenosine and its incorporation into oligodeoxynucleotides

2-Azidodeoxyadenosine (7) was conveniently synthesized from deoxyguanosine (2) by use of a combined reagent of TMSN₃–BuONO. The structure of the tautomer of the azido derivative was determined by ¹H NMR. Reaction of 7 with iPr₂NP(OEt)₂ gave an intermediate 10 of the Staudinger reaction. Incorporation of 7 into a DNA 13mer resulted in a significant decrease of the T_m value of the DNA duplex upon hybridization with the complementary strand. The thermal stability was discussed based on the hydrogen bond energy and electrostatic repulsion.     

Direct Synthesis of Yttrium Aluminum Garnet Particles in an Inductively Coupled Radio-Frequency Plasma System

Advanced phosphor materials such as cerium-doped yttrium aluminum garnet (YAG) are of interest for a variety of applications, including light-emitting diodes. Previous studies have shown that it is difficult to produce the desired YAG phase without ex-situ annealing irrespective of the synthesis technique used. This study focuses on direct synthesis of YAG phosphor particles using an inductively coupled thermal plasma system with a ceramic tube inserted coaxially into the chamber. Numerical modeling indicates that the tube provides a more uniform high-temperature region, without flow recirculation. This is hypothesized to aid in size and phase control through selective particle collection and in-flight annealing. Experiments conducted with the tube-insertion setup indicate that phase and size control of the particles is possible to a certain extent, depending on the size of the tube. Characterization results of the synthesized particles showed that submicron-sized YAG particles are synthesized as the majority phase through the tube-insertion setup.     

Comparison of fluorescence reagents for simultaneous determination of hydroxylated phenylalanine and nitrated tyrosine by high-performance liquid chromatography with fluorescence detection

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are well-known and important contributors to oxidative and nitrosative stress in several diseases. Hydroxylated phenylalanine and nitrated tyrosine products appear to be particularly susceptible targets of oxidative and nitrosative stress. We compared fluorescence reagents for their potential use in the analysis of hydroxylated phenylalanine and nitrated tyrosine products with a high-sensitivity and high-specificity HPLC-UV-FL technique. The analytes were extracted from serum via solid-phase extraction on Waters Oasis MCX cartridges. Chromatographic separation was achieved on an ODS column (Capcell Pak MG II; 150 × 2.0 mm) using a gradient mobile phase consisting of 20 mm sodium phosphate buffer (adjusted to pH 3.0) and acetonitrile. The method quantification limit for 4-nitrophenylalanine, m-tyrosine, and 3-nitrotyrosine was 0.1 μm. The relative standard deviation of the precision and accuracy was acceptable at the spiked concentration of 0.1 μm for 4-nitrophenylalanine, m-tyrosine and 3-nitrotyrosine. The method could be used for the in vitro analysis of serum samples.     

FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics

Full-quantum mechanical fragment molecular orbital-based molecular dynamics (FMO-MD) simulations were applied to the hydration reaction of formaldehyde in water solution under neutral conditions. Two mechanisms, a concerted and a stepwise one, were considered with respect to the nucleophilic addition and the proton transfer. Preliminary molecular orbital calculations by means of polarized continuum model reaction field predicted that the hydration prefers a concerted mechanism. Because the calculated activation barriers were too high for free FMO-MD simulations to give reactive trajectories spontaneously, a More O'Ferrall-Jencks-type diagram was constructed from the statistical analysis of the FMO-MD simulations with constraint dynamics. The diagram showed that the hydration proceeds through a zwitterionic-like (ZW-like) structure. The free energy changes along the reaction coordinate calculated by means of the blue moon ensemble for the hydration and the amination of formaldehyde indicated that the hydration proceeds through a concerted process through the ZW-like structure, whereas the amination goes through a stepwise mechanism with a ZW intermediate. In inspection of the FMO-MD trajectories, water-mediated cyclic proton transfers were observed in both reactions on the way from the ZW-like structure to the product. These proton transfers also have an asynchronous character, in which deprotonation from the nucleophilic oxygen atom (or nitrogen atom for amination) precedes the protonation of the carbonyl oxygen atom. The results showed the strong advantage of the FMO-MD simulations to obtain detailed information at a molecular level for solution reactions.     

Simultaneous determination of dl-lactic acid and dl-3-hydroxybutyric acid enantiomers in saliva of diabetes mellitus patients by high-throughput LC–ESI-MS/MS

A simultaneous determination method for the enantiomers of chiral carboxylic acids by the combination of ultraperformance liquid chromatography and mass spectrometry (UPLC-MS/MS) has been developed. (S)(+)-1-(2-Pyrrolidinylmethyl)-pyrrolidine (S-PMP) was used as the derivatization reagent for the high-throughput determination of biological chiral carboxylic acids, i.e., lactic acid (LA) and 3-hydroxybutyric acid (HA). The S-PMP efficiently reacted with the carboxylic acids under mild conditions at room temperature in the presence of 2,2'-dipyridyl disulfide and triphenylphosphine. The resulting S-PMP derivatives were highly responsive in the electrospray ionization (ESI)-MS operating in the positive-ion mode and gave characteristic product ions during the MS/MS, which enabled the sensitive detection using selected reaction monitoring. The derivatization was effective for the enantiomeric separation of the chiral carboxylic acids, and the resolution values of DL-LA and DL-HA were 4.91 and 9.37, respectively. Furthermore, a rapid separation of the derivatives of DL-LA and DL-HA within 7?min was performed using the UPLC system. The limits of detection on the column were in the low femtogram range (5-12?fg). The proposed procedure was successfully applied for the determination of the D- and L-isomers of LA and HA in the saliva of diabetes mellitus (DM) patients and healthy volunteers. The D-LA in DM patients was clearly higher than that in normal subjects. The derivatization followed by UPLC-ESI-MS/MS enabled the enantiomeric separation and detection of trace amounts of LA and HA in human saliva with a simple pretreatment and small sample volume.