Updated on 2023/06/29

写真a

 
MIURA Nobuaki
 
Organization
Institute for Glyco-core Research Designated lecturer
Title
Designated lecturer

Research Interests 6

  1. glycome

  2. bioinformatics

  3. proteome

  4. metaproteome

  5. glycoscience

  6. computational chemistry

Research Areas 3

  1. Nanotechnology/Materials / Fundamental physical chemistry  / 理論化学

  2. Nanotechnology/Materials / Bio chemistry  / 分子シミュレーション・計算化学

  3. Informatics / Life, health and medical informatics  / バイオインフォマティクス・メタプロテオミクス ・グライコミクス

Research History 6

  1. Nagoya University   Institute for Glyco-core Research   Institute for Glyco-core Research Designated lecturer

    2023.6

  2. Ochanomizu University   Designated associate professor

    2013.5 - 2017.3

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    Country:Japan

  3. Hokkaido University   Designated associate professor

    2003.10 - 2012.3

  4. Hokkaido University

    2001.10 - 2003.9

  5. Tokyo Metropolitan University

    1999.4 - 2001.9

  6. 工業技術院   物質工学工業技術研究所   COE研究員

    1998.2 - 1999.3

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Education 3

  1. Hokkaido University   Graduate School, Division of Natural Science

    - 1998

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    Country: Japan

  2. Hokkaido University   Graduate School, Division of Natural Science

    - 1992

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    Country: Japan

  3. Hokkaido University   Faculty of Science

    - 1990

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    Country: Japan

 

Papers 76

  1. Exposure to brefeldin A induces unusual expression of hybrid- and complex-type free N-glycans in HepG2 cells Reviewed

    Kanako Sugiura, Yuho Kawai, Arisa Yamamoto, Hiroki Yoshioka, Yuika Kiyohara, Ayaka Iida, Yurika Ozawa, Mai Nishikawa, Nobuaki Miura, Hisatoshi Hanamatsu, Jun-ichi Furukawa, Yasuro Shinohara

    Biochimica et Biophysica Acta (BBA) - General Subjects     page: 130331 - 130331   2023.2

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bbagen.2023.130331

  2. Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics Invited Reviewed

    Nobuaki Miura, Shujiro Okuda

    Computational and Structural Biotechnology Journal   Vol. 21   page: 1140 - 1150   2023.1

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.csbj.2023.01.015

  3. Toolbox Accelerating Glycomics (TAG): Improving Large-Scale Serum Glycomics and Refinement to Identify SALSA-Modified and Rare Glycans Invited Reviewed International journal

    Nobuaki Miura, Hisatoshi Hanamatsu, Ikuko Yokota, Keiko Akasaka-Manya, Hiroshi Manya, Tamao Endo, Yasuro Shinohara, Jun-ichi Furukawa

    International Journal of Molecular Sciences   Vol. 23 ( 21 ) page: 13097 - 13097   2022.10

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    Glycans are involved in many fundamental cellular processes such as growth, differentiation, and morphogenesis. However, their broad structural diversity makes analysis difficult. Glycomics via mass spectrometry has focused on the composition of glycans, but informatics analysis has not kept pace with the development of instrumentation and measurement techniques. We developed Toolbox Accelerating Glycomics (TAG), in which glycans can be added manually to the glycan list that can be freely designed with labels and sialic acid modifications, and fast processing is possible. In the present work, we improved TAG for large-scale analysis such as cohort analysis of serum samples. The sialic acid linkage-specific alkylamidation (SALSA) method converts differences in linkages such as α2,3- and α2,6-linkages of sialic acids into differences in mass. Glycans modified by SALSA and several structures discovered in recent years were added to the glycan list. A routine to generate calibration curves has been implemented to explore quantitation. These improvements are based on redefinitions of residues and glycans in the TAG List to incorporate information on glycans that could not be attributed because it was not assumed in the previous version of TAG. These functions were verified through analysis of purchased sera and 74 spectra with linearity at the level of R2 > 0.8 with 81 estimated glycan structures obtained including some candidate of rare glycans such as those with the N,N’-diacetyllactosediamine structure, suggesting they can be applied to large-scale analyses.

    DOI: 10.3390/ijms232113097

    PubMed

  4. Evaluation of the context of downstream N- and free N-glycomic alterations induced by swainsonine in HepG2 cells. International journal

    Chie Morikawa, Kanako Sugiura, Keina Kondo, Yurie Yamamoto, Yuma Kojima, Yurika Ozawa, Hiroki Yoshioka, Nobuaki Miura, Jinhua Piao, Kazue Okada, Hisatoshi Hanamatsu, Masumi Tsuda, Shinya Tanaka, Jun-Ichi Furukawa, Yasuro Shinohara

    Biochimica et biophysica acta. General subjects     page: 130168 - 130168   2022.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    Swainsonine (SWA), a potent inhibitor of class II α-mannosidases, is present in a number of plant species worldwide and causes severe toxicosis in livestock grazing these plants. The mechanisms underlying SWA-induced animal poisoning are not fully understood. In this study, we analyzed the alterations that occur in N- and free N-glycomic upon addition of SWA to HepG2 cells to understand better SWA-induced glycomic alterations. After SWA addition, we observed the appearance of SWA-specific glycomic alterations, such as unique fucosylated hybrid-type and fucosylated M5 (M5F) N-glycans, and a remarkable increase in all classes of Gn1 FNGs. Further analysis of the context of these glycomic alterations showed that (fucosylated) hybrid type N-glycans were not the precursors of these Gn1 FNGs and vice versa. Time course analysis revealed the dynamic nature of glycomic alterations upon exposure of SWA and suggested that accumulation of free N-glycans occurred earlier than that of hybrid-type N-glycans. Hybrid-type N-glycans, of which most were uniquely core fucosylated, tended to increase slowly over time, as was observed for M5F N-glycans. Inhibition of swainsonine-induced unique fucosylation of hybrid N-glycans and M5 by coaddition of 2-fluorofucose caused significant increases in paucimannose- and fucosylated paucimannose-type N-glycans, as well as paucimannose-type free N-glycans. The results not only revealed the gross glycomic alterations in HepG2 cells induced by swainsonine, but also provide information on the global interrelationships between glycomic alterations.

    DOI: 10.1016/j.bbagen.2022.130168

    PubMed

  5. Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. International journal

    Hayato Takihara, Nobuaki Miura, Kiyoko F Aoki-Kinoshita, Shujiro Okuda

    BMC bioinformatics   Vol. 22 ( 1 ) page: 505 - 505   2021.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    BACKGROUND: Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the microbiome in the environment is unclear. METHODS: Sequence alignment was performed between known glycan-related genes and complete genomes of microorganisms, and optimal parameters for identifying glycan-related genes were determined based on the alignments. Using the constructed scheme (> 90% of identity and > 25 aa of alignment length), glycan-related genes in various environments were identified from 198 different metagenome data. RESULTS: As a result, we identified 86.73 million glycan-related genes from the metagenome data. Among the 12 environments classified in this study, the percentage of glycan-related genes was high in the human-associated environment, suggesting that these environments utilize glycan metabolism better than other environments. On the other hand, the relative abundances of both glycoside hydrolases and glycosyltransferases surprisingly had a coverage of over 80% in all the environments. These glycoside hydrolases and glycosyltransferases were classified into two groups of (1) general enzyme families identified in various environments and (2) specific enzymes found only in certain environments. The general enzyme families were mostly from genes involved in monosaccharide metabolism, and most of the specific enzymes were polysaccharide degrading enzymes. CONCLUSION: These findings suggest that environmental microorganisms could change the composition of their glycan-related genes to adapt the processes involved in acquiring energy from glycans in their environments. Our functional glyco-metagenomics approach has made it possible to clarify the relationship between the environment and genes from the perspective of carbohydrates, and the existence of glycan-related genes that exist specifically in the environment.

    DOI: 10.1186/s12859-021-04425-9

    PubMed

  6. Oral Pathobiont-Induced Changes in Gut Microbiota Aggravate the Pathology of Nonalcoholic Fatty Liver Disease in Mice Reviewed

    Kyoko Yamazaki, Tamotsu Kato, Yuuri Tsuboi, Eiji Miyauchi, Wataru Suda, Keisuke Sato, Mayuka Nakajima, Mai Yokoji-Takeuchi, Miki Yamada-Hara, Takahiro Tsuzuno, Aoi Matsugishi, Naoki Takahashi, Koichi Tabeta, Nobuaki Miura, Shujiro Okuda, Jun Kikuchi, Hiroshi Ohno, Kazuhisa Yamazaki

    Frontiers in Immunology   Vol. 12   2021.10

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    Publishing type:Research paper (scientific journal)   Publisher:Frontiers Media {SA}  

    <jats:sec><jats:title>Background &amp;amp; Aims</jats:title><jats:p>Periodontitis increases the risk of nonalcoholic fatty liver disease (NAFLD); however, the underlying mechanisms are unclear. Here, we show that gut dysbiosis induced by oral administration of <jats:italic>Porphyromonas gingivalis</jats:italic>, a representative periodontopathic bacterium, is involved in the aggravation of NAFLD pathology.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>C57BL/6N mice were administered either vehicle, <jats:italic>P. gingivalis</jats:italic>, or <jats:italic>Prevotella intermedia</jats:italic>, another periodontopathic bacterium with weaker periodontal pathogenicity, followed by feeding on a choline-deficient, l-amino acid-defined, high-fat diet with 60 kcal% fat and 0.1% methionine (CDAHFD60). The gut microbial communities were analyzed by pyrosequencing the 16S ribosomal RNA genes. Metagenomic analysis was used to determine the relative abundance of the Kyoto Encyclopedia of Genes and Genomes pathways encoded in the gut microbiota. Serum metabolites were analyzed using nuclear magnetic resonance-based metabolomics coupled with multivariate statistical analyses. Hepatic gene expression profiles were analyzed <jats:italic>via</jats:italic> DNA microarray and quantitative polymerase chain reaction.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>CDAHFD60 feeding induced hepatic steatosis, and in combination with bacterial administration, it further aggravated NAFLD pathology, thereby increasing fibrosis. Gene expression analysis of liver samples revealed that genes involved in NAFLD pathology were perturbed, and the two bacteria induced distinct expression profiles. This might be due to quantitative and qualitative differences in the influx of bacterial products in the gut because the serum endotoxin levels, compositions of the gut microbiota, and serum metabolite profiles induced by the ingested <jats:italic>P. intermedia</jats:italic> and <jats:italic>P. gingivalis</jats:italic> were different.</jats:p></jats:sec><jats:sec><jats:title>Conclusions</jats:title><jats:p>Swallowed periodontopathic bacteria aggravate NAFLD pathology, likely due to dysregulation of gene expression by inducing gut dysbiosis and subsequent influx of gut bacteria and/or bacterial products.</jats:p></jats:sec>

    DOI: 10.3389/fimmu.2021.766170

  7. Challenges in Bioinformatics Analysis for Metaproteomics Invited

    Nobuaki Miura

    Proteome Letters   Vol. 6 ( 1 ) page: 17 - 27   2021.7

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publishing type:Research paper (scientific journal)  

  8. Obesity-Related Gut Microbiota Aggravates Alveolar Bone Destruction in Experimental Periodontitis through Elevation of Uric Acid Reviewed International journal

    Keisuke Sato, Kyoko Yamazaki, Tamotsu Kato, Yumiko Nakanishi, Takahiro Tsuzuno, Mai Yokoji-Takeuchi, Miki Yamada-Hara, Nobuaki Miura, Shujiro Okuda, Hiroshi Ohno, Kazuhisa Yamazaki

    mBio   Vol. 12 ( 3 ) page: e0077121   2021.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Society for Microbiology  

    Obesity is an epidemic health issue with a rapid increase worldwide. It increases the risk of various diseases, including periodontal disease, an oral chronic infectious disease.

    DOI: 10.1128/mbio.00771-21

    PubMed

  9. Comprehensive Glycomic Approach Reveals Novel Low-Molecular-Weight Blood Group-Specific Glycans in Serum and Cerebrospinal Fluid Reviewed International journal

    Jun-ichi Furukawa, Hisatoshi Hanamatsu, Ikuko Yokota, Megumi Hirayama, Tomohiro Ando, Hiroyuki Kobayashi, Shunsuke Ohnishi, Nobuaki Miura, Kazue Okada, Shota Sakai, Kohei Yuyama, Yasuyuki Igarashi, Makoto Ito, Yasuro Shinohara, Naoya Sakamoto

    Journal of Proteome Research   Vol. 20 ( 5 ) page: 2812 - 2822   2021.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    ABO blood antigens on the human red blood cell membrane as well as different cells in various human tissues have been thoroughly studied. Anti-A and -B antibodies of IgM are present in serum/plasma, but blood group-specific glyco-antigens have not been extensively described. In this study, we performed comprehensive and quantitative serum glycomic analyses of various glycoconjugates and free oligosaccharides in all blood groups. Our comprehensive glycomic approach revealed that blood group-specific antigens in serum/plasma are predominantly present on glycosphingolipids on lipoproteins rather than glycoproteins. Expression of the ABO antigens on glycosphingolipids depends not only on blood type but also on secretor status. Blood group-specific glycans in serum/plasma were classified as type I, whereas those on RBCs had different structures including hexose and hexosamine residues. Analysis of free oligosaccharides revealed that low-molecular-weight blood group-specific glycans, commonly containing lacto-N-difucotetraose, were expressed in serum/plasma according to blood group. Furthermore, comprehensive glycomic analysis in human cerebrospinal fluid showed that many kinds of free oligosaccharides were highly expressed, and low-molecular-weight blood group-specific glycans, which existed in plasma from the same individuals, were present. Our findings provide the first evidence for low-molecular-weight blood group-specific glycans in both serum/plasma and cerebrospinal fluid.

    DOI: 10.1021/acs.jproteome.1c00056

    PubMed

  10. Profiling of host genetic alterations and intra-tumor microbiomes in colorectal cancer Reviewed International journal

    Shujiro Okuda, Yoshifumi Shimada, Yosuke Tajima, Kizuki Yuza, Yuki Hirose, Hiroshi Ichikawa, Masayuki Nagahashi, Jun Sakata, Yiwei Ling, Nobuaki Miura, Mika Sugai, Yu Watanabe, Shiho Takeuchi, Toshifumi Wakai

    Computational and Structural Biotechnology Journal   Vol. 19   page: 3330 - 3338   2021

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    Some bacteria are symbiotic in tumor tissues, and metabolites of several bacterial species have been found to cause DNA damage. However, to date, the association between bacteria and host genetic alterations in colorectal cancer (CRC) has not been fully investigated. We evaluated the association between the intra-tumor microbiome and host genetic alterations in 29 Japanese CRC patients. The tumor and non-tumor tissues were extracted from the patients, and 16S rRNA genes were sequenced for each sample. We identified enriched bacteria in tumor and non-tumor tissues. Some bacteria, such as Fusobacterium, which is already known to be enriched in CRC, were found to be enriched in tumor tissues. Interestingly, Bacteroides, which is also known to be enriched in CRC, was enriched in non-tumor tissues. Furthermore, it was shown that certain bacteria that often coexist within tumor tissue were enriched in the presence of a mutated gene or signal pathway with mutated genes in the host cells. Fusobacterium was associated with many mutated genes, as well as cell cycle-related pathways including mutated genes. In addition, the patients with a high abundance of Campylobacter were suggested to be associated with mutational signature 3 indicating failure of double-strand DNA break repairs. These results suggest that CRC development may be partly caused by DNA damage caused by substances released by bacterial infection. Taken together, the identification of distinct gut microbiome patterns and their host specific genetic alterations might facilitate targeted interventions, such as modulation of the microbiome in addition to anticancer agents or immunotherapy.

    DOI: 10.1016/j.csbj.2021.05.049

    PubMed

  11. Japan Computational Mass Spectrometry Meeting 2020 Activity Report Reviewed

    Yamamoto H, Hayakawa E, Tsugawa H, Moriya Y, Fukusaki E, Goto S, Hasumura T, Miura N, Yoshizawa A C

    J. Proteome Data and Methods   Vol. 2   page: 5 - 8   2020.12

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    Language:English   Publisher:Japanese Proteomics Society  

    The Japan Computational Mass Spectrometry (JCompMS) group was launched in 2016 as a special interest group of the Japanese Society for Bioinformatics (JSBi). It aims to facilitate research communications, protocol exchanges, and further developments of computational mass spectrometry (compMS) in Japan. JCompMS aims to organize data science projects in multi-omics utilizing mass spectrometry such as proteomics, glycomics, lipidomics and metabolomics; currently, its main activities include organizing symposia, workshops, lectures, and hackathons related to compMS research. In this report, we introduce the activities held in 2020 and review the current informatics research on omics using mass spectrometry data in Japan.

    DOI: 10.14889/jpdm.2020.0005

  12. Lactone-Driven Ester-to-Amide Derivatization for Sialic Acid Linkage-Specific Alkylamidation Reviewed International journal

    Jun-ichi Furukawa, Hisatoshi Hanamatsu, Takashi Nishikaze, Hiroshi Manya, Nobuaki Miura, Hirokazu Yagi, Ikuko Yokota, Keiko Akasaka-Manya, Tamao Endo, Motoi Kanagawa, Norimasa Iwasaki, Koichi Tanaka

    Analytical Chemistry   Vol. 92 ( 21 ) page: 14383 - 14392   2020.11

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    Sialic acid attached to nonreducing ends of glycan chains via different linkages is associated with specific interactions and physiological events. Linkage-specific derivatization of sialic acid is of great interest for distinguishing sialic acids by mass spectrometry, specifically for events governed by sialyl linkage types. In the present study, we demonstrate that α-2,3/8-sialyl linkage-specific amidation of esterified sialyloligosaccharides can be achieved via an intramolecular lactone. The method of lactone-driven ester-to-amide derivatization for sialic acid linkage-specific alkylamidation, termed LEAD-SALSA, employs in-solution ester-to-amide conversion to directly generate stable and sialyl linkage-specific glycan amides from their ester form by mixing with a preferred amine, resulting in the easy assignments of sialyl linkages by comparing the signals of esterified and amidated glycan. Using this approach, we demonstrate the accumulation of altered N-glycans in cardiac muscle tissue during mouse aging. Furthermore, we find that the stability of lactone is important for ester-to-amide conversion based on experiments and density functional theory calculations of reaction energies for lactone formation. By using energy differences of lactone formation, the LEAD-SALSA method can be used not only for the sialyl linkage-specific derivatization but also for distinguishing the branching structure of galactose linked to sialic acid. This simplified and direct sialylglycan discrimination will facilitate important studies on sialylated glycoconjugates.

    DOI: 10.1021/acs.analchem.0c02209

    PubMed

  13. p62/SQSTM1-droplet serves as a platform for autophagosome formation and antioxidative stress response Reviewed

    Kageyama S, Gudmundsson S, Sou Y-S, Ichimura Y, Tamura N, Kazuno S, Ueno, T, Miura Y, Noshiro D, Abe M, Mizushima T, Miura N, Okuda S, Motohashi H, Lee J-A, Sakimura K, Ohe T, Noda N, Waguri S, Eskelinen E-L, Komatsu M

    Nature Comm. (inpress)     2020.10

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  14. Toolbox Accelerating Glycomics (TAG): Glycan Annotation from MALDI-TOF MS Spectra and Mapping Expression Variation to Biosynthetic Pathways Invited Reviewed International journal

    Nobuaki Miura, Hisatoshi Hanamatsu, Ikuko Yokota, Kazue Okada, Jun-Ichi Furukawa, Yasuro Shinohara

    Biomolecules   Vol. 10 ( 10 ) page: 1383 - 1383   2020.9

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    Glycans present extraordinary structural diversity commensurate with their involvement in numerous fundamental cellular processes including growth, differentiation, and morphogenesis. Unlike linear DNA and protein sequences, glycans have heterogeneous structures that differ in composition, branching, linkage, and anomericity. These differences pose a challenge to developing useful software for glycomic analysis. To overcome this problem, we developed the novel Toolbox Accelerating Glycomics (TAG) program. TAG consists of three units: ‘TAG List’ creates a glycan list that is used for database searching in TAG Expression; ‘TAG Expression’ automatically annotates and quantifies glycan signals and draws graphs; and ‘TAG Pathway’ maps the obtained expression information to biosynthetic pathways. Herein, we discuss the concepts, outline the TAG process, and demonstrate its potential using glycomic expression profile data from Chinese hamster ovary (CHO) cells and mutants lacking a functional Npc1 gene (Npc1 knockout (KO) CHO cells). TAG not only drastically reduced the amount of time and labor needed for glycomic analysis but also detected and quantified more glycans than manual analysis. Although this study was limited to the analysis of N-glycans and free oligosaccharides, the glycomic platform will be expanded to facilitate the analysis of O-glycans and glycans of glycosphingolipids.

    DOI: 10.3390/biom10101383

    PubMed

  15. Analysis of the susceptibility of reducing disaccharides composed of d-glucose to glycation using the Maillard reaction and a novel sensitive method that measures the percentage of the open-ring form Reviewed

    Yasuro Shinohara, Yurika Ozawa, Akimi Okita, Koichi Kato, Taku Chiba, Nobuaki Miura, Jun-ichi Furukawa

    Carbohydrate Research   Vol. 493   page: 108019 - 108019   2020.7

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.carres.2020.108019

  16. A prospective compound screening contest identified broader inhibitors for Sirtuin 1 Reviewed International journal

    Chiba S, Ohue M, Gryniukova A, Borysko P, Zozulya S, Yasuo N, Yoshino R, Ikeda K, Shin W-H, Kihara D, Iwadate M, Umeyama H, Ichikawa T, Teramoto R, Hsin K-Y, Gupta V, Kitano H, Sakamoto M, Higuchi A, Miura N, Yura K, Mochizuki M, Ramakrishnan C, Thangakani A M, Velmurugan D, Michael Gromiha M, Nakane I, Uchida N, Hakariya H, Tan M, Nakamura H, Suzuki S D, Ito T, Kawatani M, Kudoh K, Takashina S, Yamamoto K, Moriwaki M, Oda K, Kobayashi D, Okuno T, Minami S, Chikenji G, Prathipati P, Nagao N, Mohsen A, Ito M, Mizuguchi K, Honma T, Ishida T, Hirokawa T, Akiyama Y, Sekijima M

    Scientific Reports   Vol. 9 ( 1 ) page: 19585 - 19585   2019

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    Language:English   Publishing type:Research paper (scientific journal)  

    Potential inhibitors of a target biomolecule, NAD-dependent deacetylase Sirtuin 1, were identified by a contest-based approach, in which participants were asked to propose a prioritized list of 400 compounds from a designated compound library containing 2.5 million compounds using in silico methods and scoring. Our aim was to identify target enzyme inhibitors and to benchmark computer-aided drug discovery methods under the same experimental conditions. Collecting compound lists derived from various methods is advantageous for aggregating compounds with structurally diversified properties compared with the use of a single method. The inhibitory action on Sirtuin 1 of approximately half of the proposed compounds was experimentally accessed. Ultimately, seven structurally diverse compounds were identified.

    DOI: 10.1038/s41598-019-55069-y

    PubMed

  17. Comparative Glycomic Analysis of Sialyl Linkage Isomers by Sialic Acid Linkage-Specific Alkylamidation in Combination with Stable Isotope Labeling of α2,3-Linked Sialic Acid Residues. Reviewed International journal

    Hanamatsu H, Nishikaze T, Tsumoto H, Ogawa K, Kobayashi T, Yokota I, Morikawa K, Suda G, Sho T, Nakai M, Miura N, Higashino K, Sekiya S, Iwamoto S, Miura Y, Furukawa J-I, Tanaka K, Sakamoto N

    Analytical Chemistry   Vol. 91 ( 21 ) page: 13343 - 13348   2019

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    Sialic acids form the terminal sugars in glycan chains on glycoproteins via α2,3, α2,6, or α2,8 linkages, and structural isomers of sialyl linkages play various functional roles in cell recognition and other physiological processes. We recently developed a novel procedure based on sialic acid linkage-specific alkylamidation via lactone ring opening (aminolysis-SALSA). Herein, we have investigated an isotope labeling of α2,3-linked sialic acid residues (iSALSA) using amine hydrochloride salts. One limitation of SALSA using amine hydrochloride salts may be solved by adding only tert-butylamine (t-BA) as an acid scavenger, and comparative and quantitative glycomic analyses can be performed using iSALSA. We also developed quantitative glycomic analysis using dual isotope-labeled glycans by derivatizing with aminooxy-functionalized tryptophanylarginine methyl ester (aoWR) and iSALSA at the reducing and nonreducing end, respectively. Furthermore, we demonstrate that the amount of α2,3-linked sialoglycans in serum are altered during liver fibrosis using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography MS (LC/MS) analyses. We revealed that the ratio of A33,6,6 to A3F3,6,6 was gradually decreased along with liver fibrosis progression. Therefore, these glycan alterations are potential diagnostic markers of nonalcoholic steatohepatitis (NASH) fibrosis progression.

    DOI: 10.1021/acs.analchem.9b03617

    PubMed

  18. The GlyCosmos Web Portal: glycan structures, glycogenes, glycoproteins, pathways, diseases and more! Reviewed

    Shiota Masaaki, Tsuchiya Shinichiro, Ono Tamiko, Kuoka Thukaa, Miura Nobuaki, Hiraki Aiko, Yamada Issaku, Shinmachi Daisuke, Aoki Nobuyuki P, Kim Jin-Dong, Watanabe Yu, Okuda Shujiro, Suzuki Yoshinori, Fujita Noriaki, Angata Kiyohiko, Narimatsu Hisashi, Aoki-Kinoshita Kiyoko F

    GLYCOBIOLOGY   Vol. 28 ( 12 ) page: 1070 - 1071   2018.12

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  19. Sialic Acid Linkage-Specific Derivatization of GlycoSphingolipid Glycans by Ring-Opening Aminolysis of Lactones Reviewed

    Hanamatsu H, Nishikaze T, Miura N, Piao J, Okada K, Sekiya S, Iwamoto S, Sakamoto N, Tanaka K, Furukawa J-I

    Analytical Chemistry   Vol. 90   page: 13193 - 13199   2018

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  20. Functional network in posttranslational modifications: Glyco-Net in Glycoconjugate Data Bank Reviewed

    Nobuaki Miura, Takuya Okada, Daisuke Murayama, Kazuko Hirose, Taku Sato, Ryo Hashimoto, Nobuhiro Fukushima

    Methods in Molecular Biology   Vol. 1273   page: 149 - 157   2015

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    DOI: 10.1007/978-1-4939-2343-4_11

    PubMed

  21. Fluorescence polarization-based assay using N-glycan-conjugated quantum dots for screening in hemagglutinin blockers for influenza A viruses Reviewed

    Okamatsu M, Feng F, Ohyanagi T, Nagahori N, Someya K, Sakoda Y, Miura N, Nishimura S-I, Kida H

    Journal of Virological Methods   Vol. 187 ( 2 ) page: 390 - 394   2013

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier B.V.  

    DOI: 10.1016/j.jviromet.2012.11.004

  22. Novel thiosialosides tethered to metal nanoparticles as potent influenza A virus hemagglutinin blockers Reviewed

    Feng F, Sakoda Y, Ohyanagi T, Nagahori N, Shibuya H, Okamastu M, Miura N, Kida H, Nishimura S-I

    Antiviral Chemistry & Chemotherapy   Vol. 23   page: 59 - 65   2013

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  23. Identification of novel serum biomarkers of hepatocellular carcinoma using glycomic analysis Reviewed International journal

    Kamiyama T, Yokoo H, Furukawa J-I, Kurogochi M, Togashi T, Miura N, Nakanishi K, Kamachi H, Kakisaka T, Tsuruga Y, Taketomi A, Nishimura S-I, Todo S

    Hepatology   Vol. 57 ( 6 ) page: 2314 - 2325   2013

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    Language:English   Publishing type:Research paper (scientific journal)  

    UNLABELLED: 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;).

    DOI: 10.1002/hep.26262

    PubMed

  24. Enantioselective synthesis of tripodal cyclophanes and pyridinophanes by intramolecular [2+2+2] cycloaddition Reviewed

    Shibata T, Miyoshi M, Uchiyama T, Endo K, Miura N, Monde K

    Tetrahedron   Vol. 68   page: 2679 - 2686   2012

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  25. Relationship between ATM and ribosomal protein S6 revealed by the chemical inhibition of Ser/Thr protein phosphatase Type 1 Reviewed

    Li Y, Mitsuhashia S, Ikejo M, Miura N, Kawamura T, Hamakubo T, Ubukata M

    Bioscience, Biotechnology, and Biochemistry   Vol. 76 ( 3 ) page: 486 - 494   2012

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    The optimal cellular responses to DNA damage are modulated by kinase and phosphatase. The ataxia telangiectasia mutated (ATM) is a Ser/Thr kinase which is the core of the DNA damage signaling apparatus. The Ser/Thr protein phosphatase type 1 (PP1) inhibitor, tautomycetin (TC) and an antibody to the phospho-(S/T)Q sites of the ATM substrate were used to identify the common substrates for PP1 and ATM in regulating the pathway for DNA damage response. Ribosomal protein S6 (RPS6) was first identified as a substrate for PP1 and ATM. The phosphorylation at Ser247 of RPS6 was then significantly decreased by PP1-mediated dephosphorylation immediately after UV irradiation. These results suggest that PP1 specifically dephosphorylated RPS6 at phospho-Ser247 <I>in vivo</I>. In response to DNA damage, ATM activity was finally required for the phosphorylation of RPS6 at Ser247. We propose from these results a novel mechanism for modulating the RPS6 function by PP1 and ATM which regulates cell growth and survival in response to DNA-damage stimuli.

    DOI: 10.1271/bbb.110774

    CiNii Books

    Other Link: https://jlc.jst.go.jp/DN/JALC/10000221015?from=CiNii

  26. A Strategy for neuraminidase inhibitors using mechanism-based labeling information Reviewed

    Hinou H, Miyoshi R, Takasu Y, Kai H, Kurogochi M, Arioka S, Gao X-D, Miura N, Fujitani N, Otomo S, Yoshinaga T, Fujiwara T, Noshi T, Togame H, Takemoto H, Nishimura S-I

    Chemistry an Asian Journal   Vol. 2011 ( 4 ) page: 1048 - 1056   2011

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    A potent inhibitor for Vibrio cholerae neuraminidase (VCNA) was developed by using a novel two-step strategy, a target amino acid validation using mechanism-based labeling information, and a potent inhibitor search using a focused library. The labeling information suggested the hidden dynamics of a loop structure of VCNA, which can be a potential target of the novel inhibitor. A focused library composed of 187 compounds was prepared from a 9-azide derivative of 2,3-dehydro-N-acetylneuraminic acid (DANA) to interrupt the function of the loop of the labeled residues. Inhibitor 3c showed potent inhibition properties and was the strongest inhibitor with FANA, a N-trifluoroacetyl derivative of DANA. Validation studies of the inhibitor with a detergent and a Lineweaver-Burk plot suggested that the 9-substitution group would interact hydrophobically with the target loop moiety, adding a noncompetitive inhibition property to the DANA skeleton. This information enabled us to design compound 4 having the combined structure of 3c and FANA. Compound 4 showed the most potent inhibition (Ki=73a nM, mixed inhibition) of VCNA with high selectivity among the tested viral, bacterial, and mammal neuraminidases. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

    DOI: 10.1002/asia.201000594

    Scopus

    PubMed

  27. Salvileucalin C, a novel rearranged neoclerodane diterpene from Salvia leucantha Reviewed

    Aoyagi Y, Yamazaki A, Kato R, Tobe F, Fukaya H, Nishikawa T, Nakahashi A, Miura N, Monde K, Takeya K

    Tetrahedron Letters   Vol. 52   page: 1851 - 1853   2011

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  28. Alg14 organizes the formation of a multi-glycosyltransferase complex involved in initiation of lipid-linked oligosaccharide biosynthesis Reviewed

    Lu J, Takahashi T, Ohoka A, Nakajima K-I, Hashimoto R, Miura N, Tachikawa H, Gao X-D

    Glycobiology   Vol. 22   page: 504 - 516   2011

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  29. A vibrational circular dichroism approach to the determination of the absolute configurations of flavorous 5-substituted- 2(5H)-furanones Reviewed

    Nakahashi A, Yaguchi Y, Miura N, Emura M, Monde K

    Journal of Natural Products   Vol. 74   page: 707 - 711   2011

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  30. (R)-(+)- [VCD(–)984]-4-Ethyl-4-methyloctane, a cryptochiral hydrocarbon with a quaternary chirality center. (2) vibrational CD spectra of both enantiomers and absolute configurational assignment Reviewed

    Kuwahara S, Obata K, Fujita T, Miura N, Nakahashi A, Monde K, Harada N

    European Journal of Organic Chemistry   Vol. 2010   page: 6385 - 6392   2010

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  31. Novel trivalent anti-influenza reagent Reviewed International journal

    Feng F†, Miura N†, Isoda N, Sakoda Y, Okamastu M, Kida H, Nishimura S-I

    Bioorganic & Medicinal Chemistry Letters   Vol. 20 ( 12 ) page: 3772 - 3776   2010

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    We designed and synthesized novel trivalent anti-influenza reagents. Sialyllactose was located at the terminal of each valence which aimed to block each receptor-binding site of the hemagglutinin (HA) trimer on the surface of the virus. Structural analyses were carried out with a model which was constructed with a computer simulation. A previously reported cyclic glycopeptide blocker [Ohta, T.; Miura, N.; Fujitani, N.; Nakajima, F.; Niikura, K.; Sadamoto, R.; Guo, C.-T.; Suzuki, T.; Suzuki, Y.; Monde, K.; Nishimura, S.-I. Angew. Chem. Int. Ed., 2003, 42, 5186] bound to the HA in the model. The analyses suggest that the glutamine residue in the cyclic peptide bearing Neu5Acalpha2,3Galbeta1,4Glc trisaccharide via a linker interacts with the Gln189 in HA through hydrogen bonding. The present anti-influenza reagents likely interact with a glutamine residue included in the vicinity of Gln189. A plague reduction assay of the influenza virus, A/PR/8/1934 (H1N1), was performed in MDCK cells to evaluate for the synthesized compounds to inhibit viral replication. One of the compounds showed approximately 85% inhibition at the concentration of 400 microM at 4 degrees C.

    DOI: 10.1016/j.bmcl.2010.04.060

    PubMed

  32. Functional network of glycan-related molecules: Glyco-Net in Glycoconjugate Data Bank Reviewed

    Hashimoto R, Hirose K, Sato T, Fukushima N, Miura N, Nishimura S-I

    BMC Systems Biology   Vol. 4   page: 91-1 - 91-8   2010

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:BioMed Central  

    DOI: 10.1186/1752-0509-4-91

  33. Absolute stereochemistries and structure-odor relationships of 2-substituted-3(2H)-furanones

    Emura M, Sugimoto D, Yaguchi Y, Nakahashi A, Miura N, Monde K

    9th Wartburg Symposium on Flavor Chemistry & Biology     2010

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

    Nakahashi A, Miura N, Monde K, Tsukamoto S

    Bioorganic & Medicinal Chemistry Letters   Vol. 19   page: 3027 - 3030   2009

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  35. Vibrational CD Spectroscopy as a Powerful Tool for Stereochemical Study of Cyclophynes in Solution Reviewed

    An D L, Chen Q, Fang J, Yan H, Orita A, Miura N, Nakahashi A, Monde K, Otera J

    Tetrahedron Letters   Vol. 50   page: 1689 - 1692   2009

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  36. Stereochemical study of a novel tautomeric furanone, homofuraneol Reviewed

    Monde K, Nakahashi A, Miura N, Yaguchi Y, Sugimoto D, Emura

    Chirality   Vol. 21   page: E110 - E115   2009

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

    Emura M, Yaguchi Y, Nakahashi A, Sugimoto D, Miura N, Monde K

    Journal of Agricultural and Food Chemistry   Vol. 57   page: 9909 - 9915   2009

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  38. Absolute stereochemistry of flavor related 2-substituted-3(2H)-furanones, 2,5-dimethyl- 4-hydroxy-3(2H)-furanone and analogues

    Emura M, Yaguchi Y, Sugimoto D, Nakahashi A, Miura N, Monde K

    Proceedings of the 12th Weurman Symposium   Vol. 12   page: 541 - 544   2008

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  39. Interaction between the C Termini of Alg13 and Alg14 mediate formation of the active UDP-N-Acetylglucosamie transferase complex Reviewed

    Gao X-D, Moriyama S, Miura N, Dean N, Nishimura S-I

    Journal of Biological Chemistry   Vol. 283   page: 32534 - 32541   2008

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  40. Glycoconjugate Data Bank: structures — and annotated glycan structure database and N-glycan primary structure verification service Reviewed

    Nakahara T, Hashimoto R, Nakagawa H, Monde K, Miura N, Nishimura S-I

    Nucleic Acids Research   Vol. 36   page: D368 - D371   2008

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  41. Stereochemical study of chiral tautomeric flavorous furanones by vibrational circular dichroism Reviewed

    Yaguchi Y, Nakahashi A, Miura N, Sugimoto D, Monde K, Emura M

    Organic Letters   Vol. 10   page: 4883 - 4885   2008

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  42. (R)-(+)-[VCD(+)945]-4-Ethyl-4-methyloctane, the simplest chiral saturated hydrocarbon with a quaternary stereogenic center Reviewed

    Fujita T, Obata K, Kuwahara S, Miura N, Nakahashi A, Monde K, Decatur J, Harada N

    Tetrahedron Letters   Vol. 48   page: 4219 - 4222   2007

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  43. A structure and an absolute configuration of (+)-alternamin, a new coumarin from Murraya alternans having antidote activity against snake venom Reviewed

    Min H M, Aye M, Taniguchi T, Miura N, Monde K, Ohzawa K, Nikai T, Niwa M, Takaya Y

    Tetrahedron Letters   Vol. 48   page: 6155 - 6158   2007

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  44. Stereochemical studies of sialic acid derivatives by vibrational circular dichroism Reviewed

    Nakahashi A, Taniguchi T, Miura N, Monde K

    Organic Letters   Vol. 9   page: 4741 - 4744   2007

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  45. Structural transition of a 15 amino acid residue peptide induced by GM1 Reviewed

    Fujitani N, Shimizu H, Matsubara T, Ohta T, Komata Y, Miura N, Sato T, Nishimura S-I

    Carbohydrate Research   Vol. 342   page: 1895 - 1903   2007

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  46. A theoretical study of α- and β- D-glucopyranose conformations by the density functional theory Reviewed

    Miura N, Taniguchi T, Monde K, Nishimura S-I

    Chemical Physics Letters   Vol. 419 ( 4-6 ) page: 326 - 332   2006

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.cplett.2005.11.113

  47. Conformational analysis of chiral helical perfluoroalkyl chains by VCD Reviewed

    Monde K, Miura N, Hashimoto M, Taniguchi T, Inabe T

    Journal American Chemical Society   Vol. 128   page: 6000 - 6001   2006

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  48. Absolute configurations of brominated sesquiterpenes determined from vibrational circular dichroism Reviewed

    Monde K, Taniguchi T, Miura N, Nishimura S-I

    Chirality   Vol. 18   page: 335 - 339   2006

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  49. Structural assignment of isomeric 2-aminopyridine-derivatized monosialylated biantennary N-linked oligosaccharides using negative-ion multistage tandem mass spectral matching Reviewed

    Deguchi K, Takegawa Y, Ito H, Miura N, Yoshioka S, Nagai S, Nakagawa H, Nishimura S-I

    Rapid Communications in Mass Spectrometry   Vol. 20 ( 3 ) page: 412 - 418   2006

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:John Wiley & Sons  

    DOI: 10.1002/rcm.2320

  50. Absolute configurations of endoperoxides determined by vibrational circular dichroism (VCD) Reviewed

    Monde K, Taniguchi T, Miura N, Vairappan C, Suzuki M

    Tetrahedron Letters   Vol. 47   page: 4389 - 4392   2006

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  51. Chiral cruciferous phytoalexins: preparation, absolute configuration, and biological activity Reviewed

    Monde K, Taniguchi T, Miura N, Kutschy P, Čurillová Z, Pilátová M, Mojžiš J

    Bioorganic & Medicinal Chemistry   Vol. 13   page: 5206 - 5212   2005

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  52. Rational dsign, synthesis, and characterization of novel inhibitors for human β1,4-galactosyltransferase Reviewed

    Takaya K, Nagahori N, Kurogochi M, Furuike T, Miura N, Monde K, Lee Y C, Nishimura S-I

    Journal of Medicinal Chemistry   Vol. 48   page: 6054 - 6065   2005

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  53. High-throughput protein glycomics: combined use of chemoselective glycoblotting and MALDI-TOF/TOF mass spectrometry Reviewed

    Nishimura S-I, Niikura K, Kurogochi M, Fumoto M, Hinou H, Kamitani R, Nakagawa H, Deguchi K, Miura N, Monde K, Kondo H

    Angewandte Chemie International Edition   Vol. 44   page: 91 - 96   2005

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  54. Direct observation of sugar-protein, sugar-sugar, and sugar-water complexes by using cold-spray ionization time-of-flight mass spectrometry Reviewed

    Nishimura S-I, Nagahori N, Takaya K, Tachibana Y, Miura N, Monde K

    Angewandte Chemie International Edition   Vol. 44   page: 571 - 575   2005

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  55. A characteristic CH band in VCD of methyl glycosidic carbohydrates Reviewed

    Taniguchi T, Monde K, Miura N, Nishimura S-I

    Tetrahedron Letters   Vol. 45 ( 46 ) page: 8451 - 8453   2004

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.tetlet.2004.09.108

  56. Potential energy surface and intermolecular vibrations of O2-H2O Reviewed

    Sabu A, Kondo S, Miura N, Hashimoto K

    Chemical Physics Letters   Vol. 391   page: 101 - 105   2004

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  57. Direct N-glycan profiling in the presence of tryptic peptides on MALDI-TOF by controlled ion enhancement and suppression upon glycan-selective derivatization Reviewed

    Shinohara Y, Furukawa J-I, Niikura K, Miura N, Nishimura S-I

    Analytical Chemistry   Vol. 76   page: 6989 - 6997   2004

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/ac0492766

  58. Azasugar-based MMP/ADAM inhibitors as antipsoriatic agent Reviewed

    Moriyama H, Tsukida T, Inoue Y, Yokota K, Yoshino K, Kondo H, Miura N, Nishimura S-I

    Journal of Medicinal Chemistry   Vol. 47   page: 1930 - 1938   2004

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  59. Specific band observed in VCD predicts the anomeric configuration of carbohydrates Reviewed

    Monde K, Taniguchi T, Miura N, Nishimura S-I

    Journal American Chemical Society   Vol. 126 ( 31 ) page: 9496 - 9497   2004

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    DOI: 10.1021/ja048446t

  60. Vibrational circular dichroism: Chiroptical analysis of biomolecules Reviewed

    Taniguchi T, Miura N, Nishimura S-I, Monde K

    Molecular Nutrition & Food Research   Vol. 48   page: 246 - 254   2004

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  61. Electronically excited states of sodium–water clusters Reviewed

    Schulz C P, Bobbert C, Shimosato T, Daigoku K, Miura N, Hashimoto K

    The Journal of Chemical Physics   Vol. 119   page: 11620 - 11629   2003

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  62. Preparation of cruciferous phytoalexin related metabolites, (-)-dioxibrassinin and (-)-3-cyanomethyl-3-hydroxyindole, and determination of their absolute configurations by vibrational circular dichroism (VCD) Reviewed

    Monde K, Taniguchi T, Miura N, Nishimura S-I, Harada N, Dukor R K, Nafie L A

    Tetrahedron Letters   Vol. 44 ( 32 ) page: 6017 - 6020   2003

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    DOI: 10.1016/s0040-4039(03)01513-2

  63. Multi-reference configuration interaction calculation of positronium fluoride 2,1S and 2,1P states Reviewed

    Miura N, Saito S L

    Molecular Physics   Vol. 101   page: 143 - 149   2003

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  64. Glycotentacles: Synthesis of cyclic glycopeptides toward a tailored blocker of influenza virus hemagglutinin Reviewed

    Ohta T, Miura N, Fujitani N, Nakajima F, Niikura K, Guo C-T, Suzuki T, Suzuki Y, Monde K, Nishimura S-I

    Angewandte Chemie International Edition   Vol. 42 ( 42 ) page: 5186 - 5189   2003

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Wiley  

    DOI: 10.1002/anie.200351640

  65. Electronic quenching of O(1D) by collisions with O2: A theoretical study Reviewed

    Miura N, Hashimoto K, Takahashi K, Taniguchi N, Matsumi Y

    The Journal of Chemical Physics   Vol. 116 ( 13 ) page: 5551 - 5556   2002

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    Potential energy curves of triplet states for collinear O-O-2 were calculated by ab initio CASSCF and MRSDCI methods. We found a pseudocrossing between 1 (3)Sigma(-) (6 (3)A(')) and 2 (3)Sigma(-) (7 (3)A(')) states at long O-O-2 separation. The electronic quenching reaction, O(D-1)+O-2(X (3)Sigma(g)(-))-->O(P-3)+O-2(b (1)Sigma(g)(+)), is dominated by the nonadiabatic transition via the pseudocrossing. The collision energy dependence of the quenching reaction probability, which is evaluated by Zhu and Nakamura's formula, is found to be in good agreement with experiment. (C) 2002 American Institute of Physics.

    DOI: 10.1063/1.1457433

    Web of Science

  66. Electronic states of NH4(NH3)n (n=0-4) cluster radicals Reviewed

    Daigoku K, Miura N, Hashimoto K

    Chemical Physics Letters   Vol. 346   page: 81 - 88   2001

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  67. Photodissociation spectroscopy of Li-H2O and Li-D2O Complexes Reviewed

    Takasu R, Nishikawa K, Miura N, Sabu A, Hashimoto K, Shulz C P, Hertel I V, Fuke K

    Journal of Physical Chemistry A   Vol. 105   page: 6602 - 6608   2001

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  68. Excitation energies, electron affinities and ionization potential of the transition metals (II) V, Cr and Mn Reviewed

    Osanai Y, Ishikawa H, Miura N, Noro T

    Theoretical Chemistry Accounts   Vol. 105   page: 437 - 445   2001

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  69. Theoretical study of [Na(NH3)n]-(n=1-4) Reviewed

    Hashimoto K, Kamimoto T, Miura N, Okuda R, Daigoku K

    The Journal of Chemical Physics   Vol. 113   page: 9540 - 9548   2000

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  70. Molecular mechanics with QEq-CS (charge equilibration method generalized for charge separation system) Reviewed

    Kitao O, Miura N, Ushiyama H

    Journal of Molecular Structure: THEOCHEM   Vol. 461-462   page: 239 - 247   1999

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  71. Theoretical study of the mechanism of electron transfer at photosynthetic reaction centers I. Singlet excited states of free base porphin Reviewed

    Kitao O, Ushiyama H, Miura N

    The Journal of Chemical Physics   Vol. 110   page: 2936 - 2946   1999

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  72. 分散並列処理による巨大分子系の電荷計算

    三浦信明, 建部修見, 北尾修, 長嶋雲兵, 関口智嗣

    情報処理学会研究報告ハイパフォーマンスコンピューティング   Vol. 76-4   page: 19 - 24   1999

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  73. 原子の光イオン化過程へのR行列法の応用

    三浦信明

        1998.3

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    Language:Japanese   Publishing type:Doctoral thesis  

  74. Electron affinities, excitation energies and ionization potentials of the transition metals (I) Sc and Ti Reviewed

    Miura N, Noro T, Sasaki F, Osanai Y

    Theoretical Chemistry Accounts   Vol. 99   page: 248 - 254   1998

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  75. Theoretical study of the 2s2p4 4P resonance state in the photodetachment of C- Reviewed

    Miura N, Noro T, Sasaki F

    Journal of Physics B   Vol. 30   page: 5419 - 5427   1997

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  76. Theoretical determination of energies and widths of autoionizing states of the Be atom Reviewed

    Miura N, Osanai Y, Noro T, Sasaki F

    Journal of Physics B   Vol. 29   page: 2689 - 2699   1996

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Books 6

  1. 医薬品開発におけるオミクス解析技術 : ゲノム・トランスクリプトーム・プロテオーム・メタボローム

    情報機構( Role: Joint author ,  第3章 第3節 プロテオーム解析におけるバイオインフォマティクスの役割)

    情報機構  2020.3  ( ISBN:9784865021844

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    Total pages:vii, 181p   Language:Japanese

    CiNii Books

  2. Importance of Chirality to Flavor Compounds

    Engel K-H, Gary Takeoka G( Role: Contributor ,  Vibrational CD (VCD) Spectroscopy as a Powerful Tool for Chiral Analysis of Flavor Compounds, Yaguchi Y, Nakahashi A, Miura N, Taniguchi T, Sugimoto D, Emura M, Zaizen K, Kusano Y and Monde K)

    ACS Symposium Series 1212  2015 

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    Language:English Book type:Scholarly book

  3. Methods in Molecular Biology Glycoinformatics

    Lütteke T, Frank M( Role: Contributor ,  Functional Network in Posttranslational Modifications: Glyco-Net in Glycoconjugate Data Bank, Miura N, Okada N, Murayama D, Hirose K, Sato T, Hashimoto R and Fukushima N)

    Springer  2015 

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    Language:English Book type:Scholarly book

  4. Molecular Imaging for Integrated Medical Therapy and Drug Development

    Tamaki N, Kuge Y( Role: Contributor ,  Functional and Structural Analysis Reveals Dual Function on C-Terminal α Helix of Alg13 Protein, Gao X-D, Moriyama S, Miura N and Nishimura S-I)

    Springer  2010 

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  5. Experimental Glycoscience: Glycobiology

    Taniguchi N, Suzuki A, Ito Y, Narimatsu H, Kawasaki T, Hase S( Role: Contributor ,  Glycoconjugate Data Bank, Miura N and Nishimura S-I)

    Springer  2008 

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    Language:English Book type:Scholarly book

  6. 未来を拓く糖鎖科学

    永井克彦監( Role: Contributor ,  Glycoconjugate Data Bank の開発について, 西村紳一郎, 三浦信明)

    金芳堂  2005 

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    Language:Japanese Book type:Scholarly book

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MISC 3

  1. Novel method for construction of a reference amino acid sequence database for metaproteome analysis

    三浦信明, 石濱泰, 奥田修二郎, 奥田修二郎

    日本分子生物学会年会プログラム・要旨集(Web)   Vol. 44th   2021

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  2. 血清中のスフィンゴ糖脂質および遊離オリゴ糖鎖に特異的なABO式血液型抗原の解析

    岡田 和恵, 横田 育子, 花松 久寿, 三浦 信明, 大西 俊介, 湯山 耕平, 酒井 祥太, 伊東 信, 五十嵐 靖之, 坂本 直哉, 篠原 康郎, 古川 潤一

    生命科学系学会合同年次大会   Vol. 2017年度   page: [2P - 0021]   2017.12

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    Language:Japanese   Publisher:生命科学系学会合同年次大会運営事務局  

  3. 赤外円二色性を用いた絶対配置決定 誘導化を必要としない溶液状態での絶対配置決定法

    門出健次, 三浦信明, 谷口透

    化学と生物   Vol. 47 ( 7 ) page: 455 - 458   2007

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    Language:English   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    CiNii Books

Presentations 19

  1. 大規模データベースサーチの憂鬱 -メタプロテオミクス- Invited

    三浦信明

    質量分析インフォマティクス研究会2022年(第7回)ワークショップ データ解析セッション「プロテオミクスデータ解析」  2022.4.22 

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    Event date: 2022.4

    Language:Japanese   Presentation type:Symposium, workshop panel (nominated)  

  2. 質量分析から見るグライコームの夢―グライコミクスのインフォマティクスとマルチオミックスへの取り組み― Invited

    三浦信明

    質量分析インフォマティクス研究会2020年(第5回)ワークショップ 

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    Event date: 2020.8

    Language:Japanese  

  3. 大規模グライコミクスに基づく発現解析とマイニングを支援するインフォマティクス研究

    三浦信明, 古川潤一, 朴錦花, 岡田和恵, 横山育子, 篠原康郎

    第34回糖質学会  2015.7 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  4. 大規模グライコミクスに基づく発現解析とデータマイニングを支援するインフォマティクス研究

    三浦信明, 古川潤一, 朴錦花, 岡田和恵, 横田育子

    第88回日本生化学会大会 第38回日本分子生物学会年会 合同大会  2015.12 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  5. 大規模グライコミクスにおける発現解析へのインフォマティクスからアプローチ:スフィンゴ糖脂質

    三浦信明, 古川潤一, 横田育子, 岡田和恵, 篠原康郎

    第35回日本糖質学会  2016.9 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  6. 大規模グライコミクスにおける発現解析へのインフォマティクスからのアプローチ:スフィンゴ糖脂質

    三浦信明, 花松久寿, 古川潤一, 横田育子, 岡田和恵, 篠原康郎

    第36回日本糖質学会  2017.7 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  7. 大規模グライコミクスにおける発現とマイニングへのインフォマティクスからのアプローチ -スフィンゴ糖脂質-

    三浦信明, 古川潤一, 横田育子, 岡田和恵, 篠原康郎

    第89回日本生化学会大会  2016.9 

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    Language:Japanese   Presentation type:Poster presentation  

  8. 分散並列処理による巨大分子系の電荷計算

    三浦信明, 建部修見, 北尾修, 長島雲兵, 関口智嗣

    第76回ハイパフォーマンスコンピューティング研究会  1999.5 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  9. ポストゲノム研究における糖質の計算化学とその周辺 Invited

    三浦信明

    日本化学会第2回関東支部大会  2008.9 

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    Language:Japanese   Presentation type:Oral presentation (invited, special)  

  10. フッ化アルキル鎖のらせん構造の理論計算とVCDスペクトルによる解析

    三浦信明, 橋本真維, 門出健次, 吉田昌史, 谷口透

    第37回構造有機討論会  2007.9 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  11. Theoretical study of the 2s2p4 4P resonance state in the photodetachment of C- by the R-matrix method International conference

    Miura N, Sasaki F, Noro T

    The XXI International conference on the physics of electronic and atomic collisions (XXI ICPEAC)  1999 

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    Language:English   Presentation type:Poster presentation  

  12. R行列法を用いた原子の光電離断面積の計算プログラムの作成

    三浦信明, 野呂武司

    日本物理学会1992年秋の分科会  1992.9 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  13. R行列法による多電子原子の光イオン化断面積の計算

    三浦信明

    日本物理学会1993年秋の分科会  1993.10 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  14. R行列法による原子の光イオン化断面積の計算

    三浦信明, 長内有, 野呂武司, 佐々木不可止

    日本物理学会第49回年会  1994.3 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  15. R行列法によるC-の光脱離断面積の計算

    三浦信明, 野呂武司, 佐々木不可止

    日本物理学会1997年秋の分科会  1997.1 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  16. Computational Chemicstry in Glyco-science International conference

    Miura N

    The 1st CRIS International Symposium on Computational Science and Neuroscience and The 3rd Hokudai Simulation Salon Workshop  2005 

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    Language:English   Presentation type:Oral presentation (general)  

  17. A DFT study on helical perfluoroalkyl chains International conference

    Miura N, Hashimoto M, Nakahashi A, Yoshida M, Monde K

    Chirality 2008  2008 

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    Language:English   Presentation type:Oral presentation (general)  

  18. 糖鎖のDFT法によるコンフォメーション解析と振動円二色性(VCD)スペクトルによる検証

    三浦信明, 谷口透, 門出健次, 西村紳一郎

    第17回基礎有機化学連合討論会  2004.9 

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    Language:Japanese   Presentation type:Oral presentation (general)  

  19. 糖鎖の計算化学的手法による配座解析と赤外領域円二色性(VCD)分光法によるその検証

    三浦 信明, 谷口 透, 門出 健次, 西村 紳一郎

    第53回高分子討論会  2004.9 

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    Language:Japanese   Presentation type:Oral presentation (general)  

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Research Project for Joint Research, Competitive Funding, etc. 3

  1. 質量分析と統計解析の融合によるメタプロテオミクス

    2019

    JST戦略的創造研究推進制度(研究チーム型) (戦略的基礎研究推進事業:CREST) 

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    Authorship:Other  Grant type:Competitive

  2. 大規模グライコミクスにおける発現解析への質量分析と統計解析などを用いたバイオインフォマティクスアプローチ

    2013

    共同研究 

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    Authorship:Other 

  3. in silicoスクリーニングと質量分析法を用いた酵素阻害剤等探索法の開発

    2005

    秋山記念生命科学振興財団 平成17年研究助成(奨励) 

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    Grant type:Competitive

KAKENHI (Grants-in-Aid for Scientific Research) 17

  1. 包括的組織グライコームによる糖鎖分子ネットワークの構築と老化の客観的評価

    Grant number:22H03502  2022.4 - 2026.3

    科学研究費助成事業  基盤研究(B)

    古川 潤一, 萬谷 博, 三浦 信明

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    Authorship:Coinvestigator(s) 

    申請者はこれまでに特定のサブグライコームだけではなく、種々のサブグライコームを解析する技術の開発によって、細胞や血清の包括的なグライコームを利用した網羅的なバイオマーカ探索等を行ってきた。本申請課題では、申請者が有する独自技術を基盤として組織や体液の包括的なグライコーム(全糖鎖)解析法を確立し、組織横断的な総合グライコームを明らかにする。さらに老化に伴うグライコーム変化と糖鎖合成・代謝に関わる遺伝子発現変動を統合した糖鎖分子ネットワーク変化を指標とした老化の客観的評価法について精査する。

  2. Development for automatic data analysis of large-scale glycomics

    Grant number:21K12124  2021.4 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

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    Authorship:Principal investigator 

    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

  3. インフルエンザヘマグルチニンタンパク質のpH依存性構造変化に関する理論的研究

    2015 - 2016

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    Grant type:Other

  4. インフルエンザウイルスHA蛋白質のpH依存性構造変化に関する分子シミュレーション研究

    2014 - 2015

    北海道大学人獣共通感染症リサーチセンター 一般共同研究  共同研究(国内共同研究) 

    三浦信明, 五十嵐学

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    Grant type:Other

  5. 赤外円二色法によるスタンダード・キロプティカル構造解析法の構築

    2008 - 2010

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Grant type:Competitive

  6. ホモロジモデリングによるタンパク質構造予測

    2006 - 2012

  7. 疾患早期診断のための糖鎖自動分析装置開発・糖鎖による診断システム統合ソフトウェアの開発

    2004 - 2012

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    Grant type:Competitive

  8. 疾患早期診断のための糖鎖自動分析装置開発

    2004 - 2008

    科学技術振興機構  科学技術振興機構 平成16年度先端計測分析技術・機器開発事業(機器開発プログラム) 

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    Grant type:Competitive

  9. 赤外領域円二色性スペクトルによるキラル分析法の応用研究

    2004 - 2007

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Grant type:Competitive

  10. 複合糖質の新規キラル分析法の開発

    2002 - 2004

    科学研究費助成事業  萌芽研究

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    Grant type:Competitive

  11. ヘマグルチニンブロッカーの分子設計と合成・評価による抗インフルエンザ剤の研究

    2001 - 2012

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    Grant type:Collaborative (industry/university)

  12. 生物活性物質などの絶対配置を含めた赤外円二色性分光と量子化学計算によるスペクトル予測による分子構造解明

    2001 - 2012

  13. オゾン分解サイクルにおける素過程におけるメカニズムに関する量子化学的研究

    1999 - 2001

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    Grant type:Competitive

  14. タンパク質部分電化の並列処理による高速計算法の研究

    1998 - 1999

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    Grant type:Competitive

  15. ポルフィリン分子の可視スペクトルに関する量子化学的研究

    1998 - 1999

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    Grant type:Competitive

  16. R行列法を用いた多電子原子の光イオン化スペクトルの理論計算

    1992 - 1998

  17. 遷移金属原子の電子親和力・イオン化ポテンシャル・レイキエネルギーの精密計算

    1992 - 1998

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Industrial property rights 5

  1. 活性発現メカニズムを考慮した新しい糖転移酵素阻害剤及びその製造法

    西村紳一郎, 高谷健二, 三浦信明

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    Application no:2005-504842  Date applied:2004

    Announcement no:WO2004/69855  Date announced:2004

  2. α-アミラーゼ阻害剤

    西村紳一郎, 門出健次, 内田直人, 三浦信明, 森山英樹, 前川宜彦

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    Application no:2004-211376  Date applied:2004

  3. VCDを利用した糖の分析方法

    門出健次, 谷口透, 三浦信明, 西村紳一郎

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    Application no:2003-303740  Date applied:2003

  4. 糖鎖標識試薬

    篠原康郎, 三浦信明, 古川潤一, 西村紳一郎

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    Patent/Registration no:4566604  Date issued:2010

  5. 酸触媒として機能するゼオライト類似体の簡易な製造法

    西村紳一郎, 塩野正道, 三浦信明

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    Patent/Registration no:4589869  Date issued:2010

 

Teaching Experience (Off-campus) 5

  1. 物理学II(熱力学)

    Hokkaido University)

  2. マネジメント特論

    Ochanomizu University)

  3. ライフサイエンス論(分担)

    Ochanomizu University)

  4. 予測生物学

    Ochanomizu University)

  5. 構造化学

    The University of Tokyo)

 

Social Contribution 7

  1. Sun HPC Consortium Singapore 2006

    Role(s):Lecturer

    Singapore  2006.5

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「Computational Chemistry and Bioinformatics for Glycoscience and Glycotechnology」という題目で講演

  2. 平成17年度市民キャンパス「バイオとナノが創る新しい健康・生活科学」

    Role(s):Lecturer

    北海道・札幌市  2005.10

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    Audience: College students, Graduate students, Teachers, Guardians, Researchesrs, General, Scientific, Company, Civic organization, Governmental agency

    Type:Lecture

    「コンピュータでつくる治療薬」という題目で講演

  3. CONFLEX による構造解析セミナー

    Role(s):Lecturer

    大阪  2005.5

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「CONFLEXとGaussian03(DFT)を用いた糖類のコンフォメーション解析」という題目で講演

  4. Sun HPC Consortium USA 2004

    Role(s):Lecturer

    Pittsburgh  2004.11

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「Computer Assisted Glycoscience and Glycotechnology: Computational Chemicalbiology and Glycoconjugate Data Bank」という題目で講演

  5. CONFLEX & Gaussian による構造解析セミナー

    Role(s):Lecturer

    東京  2004.11

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「CONFLEXとGaussian03(DFT)を用いた糖類のコンフォメーション解析」という題目で講演

  6. 次世代ポス トゲノム・ネットワーク交流会

    Role(s):Lecturer

    北海道・札幌市  2003.2

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「北海道におけるバイオインフォマティクス分野」という題目で講演

  7. バイオ &ITクラスター創造のための強化セミナー

    Role(s):Lecturer

    北海道・ニセコ町  2002.9

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    Audience: Researchesrs, General, Company

    Type:Seminar, workshop

    「ポストゲノム・シークエンスとITの融合」という題目で講演

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