Review Papers (Misc) -
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A novel intramolecular hydrogen bonding between a side-chain pyridine ring and an amide hydrogen of the peptide backbone in tripeptides containing the new amino acid, a,a-di(2-pyridyl)glycine.
Org. Biomol. Chem., 2, 2335-2339 2004
DOI： 10.1039/b406545j
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Synthesis of Tripeptides Containing a Very Crowded a,a-Disubstituted Glycine with Pyridine Rings by Solid-Phase Ugi Reaction.
Tetrahedron Lett, 45, 8871-8874 2004
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OPTIMIZATION OF PEPTIDE ARRAYS ON A NOVEL PROTEIN CHIP FOR A PRACTICAL PROTEIN CHARACTERIZATION SYSTEM
K. Nokihara, T. Ohyama, K. Yonemura, N. Sugioka, K. Usui, T. Ojima, H. Mihara
JOURNAL OF PEPTIDE SCIENCE 10 116 - 116 2004
Publishing type：Research paper, summary (international conference) Publisher：JOHN WILEY & SONS LTD
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Peptide microarrays using structure-based peptide libraries for protein chips
Kenji Usui, Mizuki Takahashi, Tetsunori Ojima, Masato Suzuki, Kiyoshi Nokihara, Eiichi Tamiya, Hisakazu Mihara
Peptide Revolution: Genomics, Proteomics & Therapeutics 258 - 259 2004
Publisher：AMER CHEMICAL SOC
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PROTEIN-DETECTION MICROARRAYS USING STRUCTURE-BASED DESIGNED PEPTIDE LIBRARIES
K. Usui, T. Ojima, M. Suzuki, S. Watanabe, K. Tomizaki, K. Nokihara, H. Mihara
JOURNAL OF PEPTIDE SCIENCE 10 158 - 158 2004
Publishing type：Research paper, summary (international conference) Publisher：JOHN WILEY & SONS LTD
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ペプチドアレイを用いたプロテインチップの実用化を目指した研究 Reviewed
軒原清史・大山貴史・臼井健二・米村耕一・富崎欣也・三原久和
高分子論文集 61 523 - 532 2004
Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：高分子学会
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Construction of a Phosphopeptide Array for Kinase-related Protein Detection Reviewed
鈴木正人, 臼井健二, 富崎欣也, 三原久和
日本化学会講演予稿集 84th ( 2 ) 2004
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Construction of Protein-Detection System with Peptides Containing Nucleobase Amino Acids (NBAs) Reviewed
渡辺晋也, 臼井健二, 富崎欣也, 三原久和
日本化学会講演予稿集 84th ( 2 ) 2004
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Development of Peptide-Chips Focusing on a High Throughput Protein-Detection System Reviewed
K. Nokihara, T. Ohyama, K. Usui, K. Yoneyama, M. Takahashi and H. Mihara
Innovation and Perspectives in Solid Phase Synthesis & Combinatorial Libraries 83 - 88 2004
Publishing type：Article, review, commentary, editorial, etc. (bulletin of university, research institution) Publisher：Mayflower Worldwide Limited
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Development of a practical protein-chip using designed synthetic peptide-arrays Reviewed
K Nokihara, T Ohyama, K Usui, K Yonemura, K Tomizaki, H Mihara
KOBUNSHI RONBUNSHU 61 ( 10 ) 523 - 532 2004
Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：SOC POLYMER SCIENCE JAPAN
Novel high-throughput technologies, which can replace conventional electrophoresis and mass spectroscopic analyses, are in great demand for understanding the structure-function relationships of proteins. For a practical protein-detection system, arrays with immobilized designed synthetic peptides have been constructed. Peptides were labeled with fluorescent dyes in order to achieve high sensitivity. Two different types of prototype-arrayer have been constructed: one has a micro-dispensing system and the other a spot-printing system. Combinatorial peptide libraries, which consisted of beta-loop, beta-strand and alpha-helical peptides, were constructed by improved highly efficient solid-phase synthesis. Labeled peptides were covalently immobilized on solid supports such as precision glass plates. Various proteins were characterized with these peptide-arrays using a fluorescent scanner to give the "protein fingerprint" which is characteristic of the individual proteins. The results of the present prototype system demonstrate the practicality of protein-chips as a new generation of biochips.
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Microanalysis of nucleic acids using the limulus G test
T Anada, K Koumoto, M Mizu, R Karinaga, K Sakurai, S Shinkai
ANALYTICAL SCIENCES 19 ( 12 ) 1567 - 1568 2003.12
Publisher：JAPAN SOC ANALYTICAL CHEMISTRY
The limulus G test has been used as a quantitative analysis of (1-->3)-beta-D-glucans, including schizophyllan (SPG) and curdlan. The present work extended the limulus G test to detect polynucleotide/SPG complexes. The complex showed an extremely sensitive response to the test, compared with SPG itself. The minimum concentration of the complex to show the response is almost 10-times as small as that of SPG itself, indicating the possibility to detect (1-->3)-beta-D-glucans or/and polynucleotides on the pico gram/ml scale.
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Supramolecular structure of a sugar-appended organogelator explored with synchrotron X-ray small-angle scattering
K Sakurai, Y Jeong, K Koumoto, A Friggeri, O Gronwald, S Sakurai, S Okamoto, K Inoue, S Shinkai
LANGMUIR 19 ( 20 ) 8211 - 8217 2003.9
Publisher：AMER CHEMICAL SOC
Small-angle X-ray scattering (SAXS) from an organogel system prepared from methyl 4,6-O-benzylidene-alpha-D-mannopyranoside and p-xylene was carried out with a synchrotron X-ray source at SPring-8, which revealed that hexagonally packed fibrils are formed in the gel state. The spacing between the fibrils can be evaluated to be about 60 Angstrom, and this value was almost independent of both the gelator concentration and the temperature. Furthermore, the spacing is larger than the gelator molecular size. Upon heating, this supramolecular structure completely disappeared. Time-resolved SAXS revealed that phase separation takes place initially and subsequently the hexagonal structure is formed. Wide-angle X-ray diffraction (WARD) showed that there is no crystalline peak at all and the diffraction pattern is consistent with being amorphous. H-1 NMR spectral data show that the gelator molecules still maintain thermal motion in the gel state. The present SAXS, WARD, and NMR results contrast with those of "dry gels" in which the gel fibers consist of the crystal of the gelators. Our results suggest that the solvent molecules are incorporated into the gel fiber and the present gel can be classified as a "wet gel".
DOI： 10.1021/la0346752
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ペプチドマイクロアレイ ～ペプチドライブラリを用いた新規プロテインチップの創製～
臼井健二,三原久和
Bioベンチャー 3 99 - 102 2003.8
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media) Publisher：羊土社
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遺伝子の正体：DNAとRNA
杉本直己・中野修一
化学と教育 51 ( 7 ) 398 - 401 2003.7
Publishing type：Article, review, commentary, editorial, etc. (international conference proceedings) Publisher：日本化学会
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Polysaccharide-polynucleotide complexes. Part 7. Hydrogen-ion and salt concentration dependence of complexation between schizophyllan and single-stranded homo RNAs
K Sakurai, R Iguchi, M Mizu, K Koumoto, S Shinkai
BIOORGANIC CHEMISTRY 31 ( 3 ) 216 - 226 2003.6
Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE
Schizophyllan belongs to a beta-1,3-D-glucan family, which exists as a random coil in dimethyl sulfoxide (DMSO) and as a triple helix in water, respectively. The schizophyllan single chain forms a complex with single-stranded homo RNAs in water/DMSO mixed solvents. Using circular dichroism, we studied the complexation and its stability as a function of apparent pH (pH*) in a mixed solvent system and as a function of the salt concentration. The complex is formed in the pH* range 6.5-10, and dissociated in the pH* range 4-6. Both poly(A) and poly(C) adopt a double strand in the pH* range 4-6 and a single strand in the pH* range 6.5-10. Therefore, the conformational change of each polynucleotide is responsible for dissociation/association of the complex, i.e., the single strand of the polynucleotides can form complexes, whereas the double one cannot. This result indicates that hydrogen bonding and similarity of the helix parameters are essential for the complex formation. The melting temperature of the complex reaches the maximum around 0.05 M of NaCl and KCl, and the value of the maximum temperature depends on the cation species. (C) 2003 Elsevier Science (USA). All rights reserved.
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Polysaccharide-polynucleotide complexes (15): thermal stability of schizophyllan (SPG)/poly(C) triple strands is controllable by alpha-amino acid modification
M Numata, T Matsumoto, M Umeda, K Koumoto, K Sakurai, S Shinkai
BIOORGANIC CHEMISTRY 31 ( 2 ) 163 - 171 2003.4
Publisher：ACADEMIC PRESS INC ELSEVIER SCIENCE
Schizophyllan (SPG), a beta-1,3-glucan polysaccharide which is known to form macromolecular complexes with certain polynucleotides, was modified by a reductive amination method with alpha-amino, acids (Arg, Lys, and Ser). The thermal stability of the complexes as estimated by T-m was enhanced in SPG-Arg and SPG-Lys conjugates which have pI values higher than the pH of the medium (8.0). The T-m shift increased with the increase in the percentage of alpha-amino acid introduced and the highest T-m values attained were 64 degreesC for SPG-Arg conjugate and 62 degreesC for SPG-Lys conjugate, which are higher by 13 and 11 degreesC, respectively, than those of the unmodified SPG + poly(C) complex. In the SPG-Ser conjugate with a pI lower than the medium pH (8.0), the T-m values decreased with an increase in the percentage of Ser. Formation of the macromolecular complex was no longer detected above 13.2% Ser. The findings indicate that the T-m values are easily controllable by the type and percentage of the introduced alpha-amino acids. We believe, therefore, that the present conjugates, consisting of naturally originated SPG and alpha-amino acids, provide an important lead for developing nontoxic artificial vectors and to control the affinity with polynucleotides in response to medium pH and temperature. (C) 2003 Elsevier Science (USA). All rights reserved.
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Structure-designed Peptide Microarrays for Protein-Detection Reviewed
MIHARA Hisakazu, TAKAHASHI Mizuki, USUI Kenji, OJIMA Tetsunori, NOKIHARA Kiyoshi
2002 109 - 110 2003.2
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Polysaccharide-polynucleotide complexes part 17. Solvent effects on conformational-transition of polydeoxyadenylic acid in the complexes with schizophyllan
M Mizu, K Koumoto, T Kimura, K Sakurai, S Shinkai
POLYMER JOURNAL 35 ( 9 ) 714 - 720 2003
Publisher：SOC POLYMER SCIENCE JAPAN
This paper examines the relationship between the conformation and solvent for the poly(dA)/s-SPG complex using circular dichroism in the 240-300 nm wavelength region. At the low temperature and low salt concentration, poly(dA) in the complex is estimated to take C2'-endo with a different torsional angle from the anti form. With increasing temperature, the circular dichroism (CD) spectrum starts to bear characteristics of C3'-endo and anti as a minority among the majority of C2'-endo and anti. When the salt concentration is increased, the spectrum becomes almost identical to that of the high temperature form under the non-salt condition. Therefore, addition of salt provides the identical effect to increasing temperature. DO induces the same effect as decreasing temperature.
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アンチセンス治療に向けた多糖系遺伝子キャリアー
甲元一也、水雅美、櫻井和朗、新海征治
月刊BIOINDUSTRY 20 ( 10 ) 30 - 37 2003