Yuki Matsumoto

Publications (6)14.74 Total impact

• Article: Exploration of the binding proteins of perfluorooctane sulfonate by a T7 phage display screen.

  Yuka Miyano, Senko Tsukuda, Ippei Sakimoto, Ryo Takeuchi, Satomi Shimura, Noriyuki Takahashi, Tomoe Kusayanagi, Yoichi Takakusagi, Mami Okado, Yuki Matsumoto, [......], Toshifumi Takeuchi, Shinji Kamisuki, Atsuo Nakazaki, Keisuke Ohta, Masahiko Miura, Kouji Kuramochi, Yoshiyuki Mizushina, Susumu Kobayashi, Fumio Sugawara, Kengo Sakaguchi
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  ABSTRACT: Perfluorooctane sulfonate (PFOS) is a pollutant widely found throughout nature and is toxic to animals. We created a PFOS analogue on a polyethylene glycol polyacrylamide copolymer and isolated peptides that preferentially bound the PFOS analogue using a T7 phage display system. Bioinformatic analysis using the FASTAskan program on the RELIC bioinformatics server showed several human proteins that likely bound PFOS. Among them, we confirmed binding between PFOS and a recombinant soluble form of monocyte differentiation antigen CD14 (sCD14) by a surface plasmon biosensor. Furthermore, PFOS inhibited TNF-α production induced by the sCD14 in mouse macrophage RAW264.7 cells.
  Bioorganic & medicinal chemistry 05/2012; 20(13):3985-90. · 2.82 Impact Factor
• Article: Screening of a library of T7 phage-displayed peptides identifies alphaC helix in 14-3-3 protein as a CBP501-binding site.

  Yuki Matsumoto, Yosuke Shindo, Yoichi Takakusagi, Kaori Takakusagi, Senko Tsukuda, Tomoe Kusayanagi, Hitoshi Sato, Takumi Kawabe, Fumio Sugawara, Kengo Sakaguchi
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  ABSTRACT: CBP501 is a chemically modified peptide composed of twelve unnatural d-amino acids, which inhibits Chk kinase and abrogates G2 arrest induced by DNA-damaging agents. Here we identified an alphaC helix in 14-3-3 protein as a CBP501-binding site using T7 phage display technology. An affinity selection of T7 phage-displayed peptide using biotinylated CBP501 identified a 14-mer peptide NSDCIISRKIEQKE. This peptide sequence showed similarity to a portion of the alphaC helix of human 14-3-3ε, suggesting that CBP501 may bind to this region. Surface plasmon resonance (SPR) and ELISA demonstrated that CBP501 interacts with 14-3-3ε specifically at the screen-guided region. An avidin-agarose bead pull-down assay showed that CBP501 also binds to other 14-3-3 isoforms in Jurkat cells. Among the other known Chk kinase inhibitors tested, CBP501 showed the strongest affinity for 14-3-3ε. Thus, we conclude that in addition to the direct inhibition of Chk kinase activity, CBP501 directly binds to cellular 14-3-3 proteins through alphaC helix.
  Bioorganic & medicinal chemistry 12/2011; 19(23):7049-56. · 2.82 Impact Factor
• Article: Camptothecin (CPT) directly binds to human heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and inhibits the hnRNP A1/topoisomerase I interaction.

  Daisuke Manita, Yuzuru Toba, Yoichi Takakusagi, Yuki Matsumoto, Tomoe Kusayanagi, Kaori Takakusagi, Senko Tsukuda, Kazunori Takada, Yoshihiro Kanai, Shinji Kamisuki, Kengo Sakaguchi, Fumio Sugawara
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  ABSTRACT: Camptothecin (CPT) is an anti-tumor natural product that forms a ternary complex with topoisomerase I (top I) and DNA (CPT-top I-DNA). In this study, we identified the direct interaction between CPT and human heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) using the T7 phage display technology. On an avidin-agarose bead pull down assay, hnRNP A1 protein was selectively pulled down in the presence of C20-biotinylated CPT derivative (CPT-20-B) both in vitro and in vivo. The interaction was also confirmed by an analysis on a quartz-crystal microbalance (QCM) device, yielding a K(D) value of 82.7 nM. A surface plasmon resonance (SPR) analysis revealed that CPT inhibits the binding of hnRNP A1 to top I (K(D): 260 nM) in a non-competitive manner. Moreover, an in vivo drug evaluation assay using Drosophila melanogaster showed that the knockout of the hnRNP A1 homolog Hrb87F gene showed high susceptibility against 5-50 μM of CPT as compared to a wild-type strain. Such susceptibility was specific for CPT and not observed after treatment with other cytotoxic drugs. Collectively, our data suggests that CPT directly binds to hnRNP A1 and non-competitively inhibits the hnRNP A1/top I interaction in vivo. The knockout strain loses the hnRNP A1 homolog as a both CPT-binding partner and naïve brakes of top I, which enhances the formation of the CPT-top I-DNA ternary complexes and subsequently sensitizes the growth inhibitory effect of CPT in D. melanogaster.
  Bioorganic & medicinal chemistry 10/2011; 19(24):7690-7. · 2.82 Impact Factor
• Article: Binding region and interaction properties of sulfoquinovosylacylglycerol (SQAG) with human vascular endothelial growth factor 165 revealed by biosensor-based assays

  Yoichi Takakusagi, Kaori Takakusagi, Noriko Ida, Mihoko Takami, Yuki Matsumoto, Tomoe Kusayanagi, Tadashi Nakabayashi, Satoko Aoki, Hiroshi Murata, Keisuke Ohta, Fumio Sugawara, Kengo Sakaguchi
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  ABSTRACT: Sulfoquinovosylacylglycerol (SQAG) is a sulfoglycolipid showing anti-angiogenic and radiosensitizing effects for treatment of solid tumors both in vitro and in vivo. Here we elucidated the interaction of SQAG with various growth factors and their cognate receptors for vascular formation using biosensor-based assays. The structure–binding relationship was also determined. Our results show that βSQDG selectively recognizes heparin binding domain (HBD) in human vascular endothelial growth factor 165 (hVEGF165) with an affinity in the order of 10−11 M. The presence of both a sulfate moiety and at least one C18 length fatty acid chain is essential for binding. Conversion of anomeric configurations in SQAG did not alter the affinity with hVEGF165. This SQAG association inhibited T7 phage -displayed HBD binding to neuropilin-1 (NRP1), a VEGF receptor on the endothelial cell surface of blood vessels that specifically recognizes HBD in hVEGF165.
  MedChemComm. 01/2011; 2:1188-1193.
• Article: Identification of trimannoside-recognizing peptide sequences from a T7 phage display screen using a QCM device.

  Kazusa Nishiyama, Yoichi Takakusagi, Tomoe Kusayanagi, Yuki Matsumoto, Shiori Habu, Kouji Kuramochi, Fumio Sugawara, Kengo Sakaguchi, Hideyo Takahashi, Hideaki Natsugari, Susumu Kobayashi
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  ABSTRACT: Here, we report on the identification of trimannoside-recognizing peptide sequences from a T7 phage display screen using a quartz-crystal microbalance (QCM) device. A trimannoside derivative that can form a self-assembled monolayer (SAM) was synthesized and used for immobilization on the gold electrode surface of a QCM sensor chip. After six sets of one-cycle affinity selection, T7 phage particles displaying PSVGLFTH (8-mer) and SVGLGLGFSTVNCF (14-mer) were found to be enriched at a rate of 17/44, 9/44, respectively, suggesting that these peptides specifically recognize trimannoside. Binding checks using the respective single T7 phage and synthetic peptide also confirmed the specific binding of these sequences to the trimannoside-SAM. Subsequent analysis revealed that these sequences correspond to part of the primary amino acid sequence found in many mannose- or hexose-related proteins. Taken together, these results demonstrate the effectiveness of our T7 phage display environment for affinity selection of binding peptides. We anticipate this screening result will also be extremely useful in the development of inhibitors or drug delivery systems targeting polysaccharides as well as further investigations into the function of carbohydrates in vivo.
  Bioorganic & medicinal chemistry 12/2008; 17(1):195-202. · 2.82 Impact Factor
• Article: Selective adsorption of bacterial cells onto zeolites.

  Munehiro Kubota, Tadashi Nakabayashi, Yuki Matsumoto, Tohru Shiomi, Yusuke Yamada, Keita Ino, Hiroyuki Yamanokuchi, Masayoshi Matsui, Tatsuo Tsunoda, Fujio Mizukami, Kengo Sakaguchi
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  ABSTRACT: Zeolites adsorb microbial cells on their surfaces and selective adsorption for specific microorganisms was seen with certain zeolites. Tests for the adsorption ability of zeolites were conducted using various established microbial cell lines. Specific cell lines were shown to selectively absorb to certain zeolites, species to species. In order to understand the selectivity of adsorption, we tested adsorption under various pH conditions and determined the zeta-potentials of zeolites and cells. The adsorption of some cell lines depended on the pH, and some microorganisms were preferentially adsorbed at acidic pH. The values of zeta-potentials were used for calculating the electric double layer interaction energy between zeolites and microbial cells. There was a correlation between the experimental adsorption results and the interaction energy. Moreover, we evaluated the surface hydrophobicity of bacterial cells by using the microbial adherence to hydrocarbon (MATH) assay. In addition, we also applied this method for zeolites to quantify relative surface hydrophobicity. As a result, we found a correlation between the adsorption results and the hydrophobicity of bacterial cells and zeolites. These results suggested that adsorption could be explained mainly by electric double layer interactions and hydrophobic interactions. Finally, by using the zeolites Na-BEA and H-Y, we succeeded in clearly separating three representative microbes from a mixture of Escherichia coli, Bacillus subtilis and Staphylococcus aureus. Zeolites could adsorb each of the bacterial cell species with high selectivity even from a mixed suspension. Zeolites can therefore be used as effective carrier materials to provide an easy, rapid and accurate method for cell separation.
  Colloids and Surfaces B Biointerfaces 07/2008; 64(1):88-97. · 3.46 Impact Factor