Papers -
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SPR sensor chip for detection of small molecules using molecularly imprinted polymer with embedded gold nanoparticles.
三好大輔
Anal Chem ( 77 ) 4282 - 4285 2005.11
Single Work
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Roles of Mg2+ in TPP-dependent riboswitch.
三好大輔
FEBS Lett ( 579 ) 2583 - 2588 2005.11
Single Work
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Thermodynamic and Kinetic Analysis of Nucleic Acid Structures toward Pharmacogenomics
三好大輔
Current Pharmacogenomics ( 3 ) 217 - 236 2005.11
Single Work
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Drastic effect of a single base difference between human and tetrahymena telomere sequences on their structures under molecular crowding conditions.
三好大輔
Angew Chem Int Ed Engl. ( 44 ) 3740 - 3744 2005.11
Single Work
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SPR Sensor Chip for Detection of Small Molecules Using Molecularly Imprinted Polymer with Embedded Gold Nanoparticles Anal. Chem.
松井淳
（学術雑誌、 2005 ）77, 4282-4285 4282 - 4285 2005.11
Single Work
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Synthesis of Water-soluble Porphyrin and the Corresponding Highly Planar Benzoporphyrin without meso-Substituents.
村嶋 貴之
Tetrahedron Lett., 2005.11
Single Work
Tetrahedron Lett., （学術雑誌、2005）46, 113-116.
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Resolution of Non-protein Amino Acids via Carica papaya Lipase-catalyzed Enantioselective Transesterification.
村嶋 貴之
Tetrahedron: Asymmetry, 2005.11
Single Work
Tetrahedron: Asymmetry, （学術雑誌、2005）16, 2569-2573.
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Enzymatic Resolution of 2-Aryloxy-1-propanols via Lipase-catalyzed Enantioselective Acylation Using Acid Anhydrides as Acyl Donors.
村嶋 貴之
J. Mol. Cat., B, 2005.11
Single Work
J. Mol. Cat., B, （学術雑誌、2005）37, 63-67.
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Studies on intramolecular hydrogen bonding between the pyridine nitrogen and the amide hydrogen of the peptide: synthesis and conformational analysis of tripeptides containing novel amino acids with a pyridine ring.
村嶋 貴之
J. Peptide Sci., 2005.11
Single Work
J. Peptide Sci., （学術雑誌、2005）11, 491-498.
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Conformational switch of oligonucleotides induced by spermine
中野 修一
Nucleic Acids Symp. Ser. 49 241 - 242 2005.11
Single Work
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Linkage between proton binding and folding in RNA: implications for RNA catalysis
中野 修一
Biochem. Soc. Trans. 33 466 - 470 2005.11
Single Work
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Kenji Usui, Tetsunori Ojima, Kin-Ya Tomizaki, Hisakazu Mihara
Nanobiotechnology 1 ( 2 ) 191 - 199 2005.11
For the realization of a practical high-throughput protein detection and analysis system, a novel peptide array has been constructed using a designed glycopeptide model library with an α-helical secondary structure. This study will contribute the increment of the diversity of such an array system and the application to focused proteomics and ligand screening by effective detection of sugar-binding proteins. Fluorescent glycopeptides with an α-helix, a β-strand, or a loop structure were designed initially to select a suitable scaffold for the detection of a model protein. After selection of the α-helical structure as the best scaffold, a small model library with various saccharides was constructed to have charge and hydrophobicity variations in the peptide sequences. When various sugar-binding proteins were added to the peptide library array, the fluorescent peptides showed different responses in fluorescence intensities depending on their sequences as well as saccharides. The patterns of these responses could be regarded as "protein fingerprints" (PFPs), which are able to establish the identities of the target proteins. The resulting PFPs reflected the recognition properties of the proteins. Furthermore, statistical data analysis from obtained PFPs was performed using a cluster analysis. The PFPs of sugar-binding proteins were clustered successfully depending on their families and binding properties. These studies demonstrate that arrays with glycopeptide libraries based on designed structures can be promising tools to detect and analyze the target proteins. Designed peptides with functional groups such as sugars will play roles as the capturing agents of high-throughput protein nano/micro arrays for focused proteomics and ligand screening studies. Copyright © 2005 Humana Press Inc. All rights of any nature whatsoever are reserved.
DOI： 10.1385/NBT:1:2:191
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Difference in self-assembling morphology of peptide nanorings Reviewed
H Okamoto, T Yamada, H Miyazaki, T Nakanishi, K Takeda, K Usui, Obataya, I, H Mihara, H Azehara, W Mizutani, K Hashimoto, H Yamaguchi, Y Hirayama
JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS 44 ( 11 ) 8240 - 8248 2005.11
Publisher：JAPAN SOC APPLIED PHYSICS
We synthesized the peptide nanorings of cyclo[-(D-Ala-L-Gln)(3)], cyclo[-(D-CyS-L-Gln)(3)], CyC10[-D-Cys-L-HiS-D-Ala-L-Asn-Gly-L-Gln-1 and Cyc1o[-(L-Gln)(5)], and studied the way in which the difference in the type and/or number of component amino acid residues changes the self-assembling morphology of the nanorings on gold substrates by atomic force microscopy. The study revealed that CyClo[-(D-Ala-L-Gln)(3)] formed nanotube bundles through inter-ring hydrogen bonds, while the nanorings of CyC10[-(D-CyS-L-Gln)3] adhered to the gold surface directly due to the high affinity of thiol to gold. In contrast, a random amino acid sequence of cyclo[-D-CyS-L-HiS-D-Ala-L-Asn-GlY-L-Gln-] resulted in many isolated nanotubes, which were first observed in the present study. While the D,L-peptide nanotubes have very straight forms, the homo-L-peptide of cyclo[-(L-Gln)(5)] formed interesting randomly branching nanotubes that were entwined and grew on the substrate. Scanning tunneling microscopy was also performed and high-resolution images of both the peptide nanotubes and the nanotube bundles were obtained.
DOI： 10.1143/JJAP.44.8240
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IR study on stacking manner of peptide nanorings in peptide nanotubes Reviewed
Y Nagai, T Nakanishi, H Okamoto, K Takeda, Y Furukawa, K Usui, H Mihara
JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS 44 ( 10 ) 7654 - 7661 2005.10
Publisher：JAPAN SOC APPLIED PHYSICS
We here report our theoretical as well as experimental studies on the stacking manner of peptide nanorings (PNRs) in peptide nanotubes (PNTs). We focus on the molecular vibrations of N-H and C=O stretching modes and discuss this subject via their infrared (IR) spectroscopy, because PNTs are formed by the inter-ring H bonds between the adjacent PNRs via -N-H(...)O=C-. Symmetry analysis based on group theory reveals that parallel stacking causes two IR active modes in these molecular vibrations while three modes are active in the antiparallel stacking. This difference in the number of IR active modes is determined only by the stacking manner and not by the number of amino acid residues composing the PNRs. By using two typical PNRs Of cyclo[-((L)-Gln-D-Ala)(3)] and cyclo[-((L)-Gln-(D)-Ala)(4)], we further studied the favorable stacking manners of PNRs via IR observation. Our IR experiments as well as the ab initio energetics show that the former PNRs create a PNT by stacking themselves in parallel while the latter PNRs do so by stacking themselves in an antiparallel manner.
DOI： 10.1143/JJAP.44.7654
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Specific recognition of the basic N peptide by an RNA（共著）
J. Kawakami, H. Tokitoh, Y. Tanabe, and N. Sugimoto
Nucleic Acids Symposium Series 49 353 - 354 2005.9
Joint Work
Authorship：Lead author
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Central dogma for a molecular design based on DNA: DNB (databasing/designable nanobio) -> ENB (engineering nanobio) -> FNB (functional nanobio) Reviewed
S. Nakano and N. Sugimoto
Chemistry Letters 34 1206 - 1211 2005.7
Single Work
DOI： 10.1246/cl.2005.1206
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Protein-detecting microarrays: Current accomplishments and requirements Reviewed
Kin-Ya Tomizaki, Kenji Usui, Hisakazu Mihara
ChemBioChem 6 ( 6 ) 782 - 799 2005.5
Joint Work
The sequencing of the human genome has been successfully completed and offers the chance of obtaining a large amount of valuable information for understanding complex cellular events simply and rapidly in a single experiment. Interestingly, in addressing these proteomic studies, the importance of protein-detecting microarray technology is increasing. In the coming few years, microarray technology will become a significantly promising and indispensable research/diagnostic tool from just a speculative technology. It is clear that the protein-detecting microarray is supported by three independent but strongly related technologies (surface chemistry, detection methods, and capture agents). Firstly, a variety of surface-modification methodologies are now widely available and offer site-specific immobilization of capture agents onto surfaces in such a way as to keep the native conformation and activity. Secondly, sensitive and parallel detection apparatuses are being developed to provide highly engineered microarray platforms for simultaneous data acquisition. Lastly, in the development of capture agents, antibodies are now probably the most prominent capture agents for analyzing protein abundances. Alternative scaffolds, such as phage-displayed antibody and protein fragments, which provide the advantage of increasing diversity of proteinic capture agents, however, are under development. An approach involving recombinant proteins fused with affinity tag(s) and coupled with a highly engineered surface chemistry wilt provide simple production protocols and specific orientations of capture agents on the -microarray formats. Peptides and other small molecules can be employed in screening highly potent ligands as well as in measuring enzymatic activities. Protein-detecting microarrays supported by the three key technologies should contribute in accelerating diagnostic/biological research and drug discovery. © 2005 Wiley-VCH Verlag GmbH &
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Studies on Fluorescent Dyes and Surface Chemistry focusing on Practical Peptide Array Preparation Reviewed
NOKIHARA Kiyoshi, USUI Kenji, YONEMURA Koichi, OHYAMA Takafumi, OKA Yasuo, TOMIZAKI Kin‐ya, MIHARA Hisakazu
Pept Sci 2004 145 - 148 2005.3
Joint Work
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Tyrosine phosphorylation of adaptor protein 3BP2 induces T cell receptor-mediated activation of transcription factor.
Qu X, Kawauchi-Kamata K, Miah SM, Hatani T, Yamamura H, Sada K
Biochemistry 44 ( 10 ) 3891 - 3898 2005.3
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Thermodynamic analysis of duplex formation of the heterochiral DNA with L-deoxyadenosine（共著） Reviewed
J. Kawakami, K. Tsujita, and N. Sugimoto
Analytical Sciences 21 ( 2 ) 77 - 82 2005.2
Joint Work
Authorship：Lead author