Nobuaki Miura

Identification of novel serum biomarkers of hepatocellular carcinoma using glycomic analysis.

The altered N‐glycosylation of glycoproteins has been suggested to play an important role in the behavior of malignant cells. Using glycomics technology, we attempted to determine the specific and detailed N‐glycan profile for hepatocellular carcinoma (HCC) and investigate the prognostic capabilities. From 1999 to 2011, 369 patients underwent primary curative hepatectomy in our facility and were followed up for a median of 60.7 months. As normal controls, 26 living Japanese related liver transplantation donors were selected not infected by hepatitis B and C virus. Their mean age was 40.0 and 15 (57.7%) were male. We used a glycoblotting method to purify N‐glycans from preoperative blood samples from this cohort (10 μL serum) which were then identified and quantified using mass spectrometry (MS). Correlations between the N‐glycan levels and the clinicopathologic characteristics and outcomes for these patients were evaluated. Our analysis of the relative areas of all the sugar peaks identified by MS, totaling 67 N‐glycans, revealed that a proportion had higher relative areas in the HCC cases compared with the normal controls. Fourteen of these molecules had an area under the curve of greater than 0.80. Analysis of the correlation between these 14 N‐glycans and surgical outcomes by univariate and multivariate analysis identified G2890 (m/z value, 2890.052) as a significant recurrence factor and G3560 (m/z value, 3560.295) as a significant prognostic factor. G2890 and G3560 were found to be strongly correlated with tumor number, size, and vascular invasion. Conclusion: Quantitative glycoblotting based on whole serum N‐glycan profiling is an effective approach to screening for new biomarkers. The G2890 and G3560 N‐glycans determined by tumor glycomics appear to be promising biomarkers for malignant behavior in HCCs. (HEPATOLOGY 2013;)

Electronically Excited States of Sodium-Water-Clusters

The lowest electronically excited state of small Na(H2O)n clusters has been investigated experimentally and theoretically. The excitation energy as determined by the depletion spectroscopy method drops from 16 950 cm−1 for the sodium atom down to 9670 cm−1 when only three water molecules are attached to the Na atom. For larger clusters the absorption band shifts back towards higher energies and reaches 10 880 cm−1 for n=12. The experimental data are compared to quantum-chemical calculations at the Moeller–Plesset second-order perturbation and multireference single and double excitation configuration interaction levels. We found that the observed size dependence of the transition energy is well reproduced by the interior structure where the sodium atom is surrounded by water molecules. The analysis of the radial charge distribution of the unpaired electron in these interior structures gives a new insight into the formation of the “solvated” electron.

Glycoconjugate Data Bank:Structures—an annotated glycan structure database and N-glycan primary structure verification service

Glycobiology has been brought to public attention as a frontier in the post-genomic era. Structural information about glycans has been accumulating in the Protein Data Bank (PDB) for years. It has been recognized, however, that there are many questionable glycan models in the PDB. A tool for verifying the primary structures of glycan 3D structures is evidently required, yet there have been no such publicly available tools. The Glycoconjugate Data Bank:Structures (GDB:Structures, http://www.glycostructures.jp) is an annotated glycan structure database, which also provides an N-glycan primary structure (or glycoform) verification service. All the glycan 3D structures are detected and annotated by an in-house program named ‘getCARBO’. When an N-glycan is detected in a query coordinate by getCARBO, the primary structure of the glycan is compared with the most similar entry in the glycan primary structure database (KEGG GLYCAN), and unmatched substructure(s) are indicated if observed. The results of getCARBO are stored and presented in GDB:Structures.

Alg14 organizes the formation of a multiglycosyltransferase complex involved in initiation of lipid-linked oligosaccharide biosynthesis

Protein N-glycosylation begins with the assembly of a lipid-linked oligosaccharide (LLO) on the endoplasmic reticulum (ER) membrane. The first two steps of LLO biosynthesis are catalyzed by a functional multienzyme complex comprised of the Alg7 GlcNAc phosphotransferase and the heterodimeric Alg13/Alg14 UDP-GlcNAc transferase on the cytosolic face of the ER. In the Alg13/14 glycosyltransferase, Alg14 recruits cytosolic Alg13 to the ER membrane through interaction between their C-termini. Bioinformatic analysis revealed that eukaryotic Alg14 contains an evolved N-terminal region that is missing in bacterial orthologs. Here, we show that this N-terminal region of Saccharomyces cerevisiae Alg14 localize its green fluorescent protein fusion to the ER membrane. Deletion of this region causes defective growth at 38.5°C that can be partially complemented by overexpression of Alg7. Coimmunoprecipitation demonstrated that the N-terminal region of Alg14 is required for direct interaction with Alg7. Our data also show that Alg14 lacking the N-terminal region remains on the ER membrane through a nonperipheral association, suggesting the existence of another membrane-binding site. Mutational studies guided by the 3D structure of Alg14 identified a conserved α-helix involved in the second membrane association site that contributes to an integral interaction and protein stability. We propose a model in which the N- and C-termini of Alg14 coordinate recruitment of catalytic Alg7 and Alg13 to the ER membrane for initiating LLO biosynthesis.

Preparation of cruciferous phytoalexin related metabolites, (−)-dioxibrassinin and (−)-3-cyanomethyl-3-hydroxyoxindole, and determination of their absolute configurations by vibrational circular dichroism (VCD)

Abstract Cruciferous phytoalexin related metabolites, (−)-dioxibrassinin ( 1 ) and (−)-3-cyanomethyl-3-hydroxyoxindole ( 2 ) were prepared from isatin as racemates and were resolved by chiral HPLC. Their absolute configurations were determined by the new chiroptical technique, vibrational circular dichroism (VCD), as well as by the conventional electronic circular dichroism (ECD). It is concluded that the absolute configurations of the naturally occurring (−)- 1 and (−)- 2 are both S.

A Vibrational Circular Dichroism Approach to the Determination of the Absolute Configurations of Flavorous 5-Substituted-2(5H)-furanones

Sotolon (1) and maple furanone (2) are naturally occurring chiral furanones. These 5-substituted-2(5H)-furanones are industrially significant aroma compounds due to their characteristic organoleptic properties and extraordinarily low odor thresholds. Each enantiomer of 1 and 2 was successfully obtained by preparative enantioselective supercritical fluid chromatography. The absolute configuration of 1 was confirmed as (R)-(-)-1 and (S)-(+)-1 by adopting the vibrational circular dichroism (VCD) approach. The absolute configuration of 2, which has remained ambiguous since its discovery in 1957, was determined as (R)-(+)-2 and (S)-(-)-2 for the first time by the VCD technique. Surprisingly, the signs of the optical rotation of 2 are opposite of those of 1 regardless of their identical absolute configurations. This observation emphasizes the risk in absolute configurational assignments based on comparison of optical rotation signs of similar structures. Odor evaluation of the enantiomers of 2 revealed different odor intensities.

Interaction between the C Termini of Alg13 and Alg14 Mediates Formation of the Active UDP-N-acetylglucosamine Transferase Complex

The second step of eukaryotic N-linked glycosylation in endoplasmic reticulum is catalyzed by an UDP-N-acetylglucosamine transferase that is comprised of two subunits, Alg13 and Alg14. The interaction between Alg13 and 14 is crucial for UDP-GlcNAc transferase activity, so formation of the Alg13/14 complex is likely to play a key role in the regulation of N-glycosylation. Using a combination of bioinformatics and molecular biological methods, we have undertaken a functional analysis of yeast Alg13 and Alg14 proteins to elucidate the mechanism of their interaction. Our mutational studies demonstrated that a short C-terminal α-helix of Alg13 is required for interaction with Alg14 and for enzyme activity. Electrostatic surface views of the modeled Alg13/14 complex suggest the presence of a hydrophobic cleft in Alg14 that provides a pocket for the Alg13 C-terminal α-helix. Co-immunoprecipitation assays confirmed the C-terminal three amino acids of Alg14 are required for maintaining the integrity of Alg13/Alg14 complex, and this depends on their hydrophobicity. Modeling studies place these three Alg14 residues at the entrance of the hydrophobic-binding pocket, suggesting their role in the stabilization of the interaction between the C termini of Alg13 and Alg14. Together, these results demonstrate that formation of this hetero-oligomeric complex is mediated by a short C-terminal α-helix of Alg13 in cooperation with the last three amino acids of Alg14. In addition, deletion of the N-terminal β-strand of Alg13 caused the destruction of protein, indicating the structural importance of this region in protein stability.

Electronic states of NH4(NH3)n(n=0–4) cluster radicals

Abstract We have investigated geometries, ionization potentials (IPs), and vertical transition energies (VTEs) of NH 4 ( NH 3 ) n (n=0–4) cluster radicals by ab initio MO method at the correlated level. The structures in which NH 4 donates as many NH bonds as possible to the hydrogen bonding with surrounding NH 3 molecules are the most stable for each n . The calculated IPs agree well with experiment. The spatial expansion of the unpaired electron occurs with stepwise solvation. The growing one-center Rydberg-like nature of the cluster radicals results in the successive decrease in the transition energies to the low-lying excited states, which is responsible for the red shifts of the electronic absorption bands.

Stereochemical studies of hexylitaconic acid, an inhibitor of p53-HDM2 interaction.

Hexylitaconic acid (1) is an intriguing natural product possessing a chiral carbon, and both its enantiomers have been found in nature. Enantiomeric pure (+)-(1) and (-)-(1) were successfully prepared by racemic synthesis followed by enantiomeric separation in a chiral HPLC system. Their absolute configurations were clarified by the vibrational circular dichroism technique using their methyl esters 2 and lactones 3. Their inhibitory activities against the interaction of p53-HDM2 were also examined.

Stereochemical studies of odorous 2-substituted-3(2H)-furanones by vibrational circular dichroism.

Chiral naturally occurring aroma compounds often exhibit enantiomeric excesses due to their stereoselective biogenesis. In general, significant organoleptic differences are perceived between these enantiomers. Chiral 2-substituted-3(2H)-furanones, featuring a unique keto-enol tautomer, the cause of their racemization, have been known to play an important role in flavor because of their extremely low threshold values and their burnt sugar odor characteristics. Since the discovery of these important aroma chemicals, they have been used in large quantities as raw materials in the flavor and fragrance industry. However, absolute configurations of these furanone derivatives have remained ambiguous for the past 40 years. Here optical resolutions of 2,5-dimethyl-4-hydroxy-3(2H)-furanone, 2,5-dimethyl-4-methoxy-3(2H)-furanone, and 4-acetoxy-2,5-dimethyl-3(2H)-furanone were accomplished using chiral CO(2) supercritical fluid chromatography (SFC). Their absolute configurations were unraveled for the first time using the vibrational circular dichroism (VCD) technique as well as by chemical relay reactions. Odor evaluation of each enantiomer revealed relationships between their configurations and odor activities.