Experts and Doctors on binding sites in Tokushima, Japan


Locale: Tokushima, Japan
Topic: binding sites

Top Publications

  1. Yoshida T, Munei Y, Hitaoka S, Chuman H. Correlation analyses on binding affinity of substituted benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on their complex structures. J Chem Inf Model. 2010;50:850-60 pubmed publisher
    ..The proposed procedure was demonstrated to provide a quantitative basis for understanding a ligand-protein interaction at electronic and atomic levels. ..
  2. Umehara A, Nishioka M, Obata T, Ebina Y, Shiota H, Hashida S. A novel ultra-sensitive enzyme immunoassay for soluble human insulin receptor ectodomain and its measurement in urine from healthy subjects and patients with diabetes mellitus. Clin Biochem. 2009;42:1468-75 pubmed publisher
    ..7+/-20.1 pg/mg creatinine) was significantly higher than those in healthy volunteers (1.4+/-0.9; P<0.001). ICT-EIA for sIRalpha may be useful as a good marker for evaluating diabetes risk. ..
  3. Kobayashi K, Nagahama M, Ohkubo N, Kojima T, Shirai H, Iwamoto S, et al. Role of Ca2+-binding motif in cytotoxicity induced by Clostridium perfringens iota-toxin. Microb Pathog. 2008;44:265-70 pubmed
    ..The result indicates that the conserved Ca(2+)-binding motif in the N-terminal region of Ib plays a role in the interaction of Ib with Ia in the presence of Ca(2+). ..
  4. Wu X, Yano M, Washida H, Kido H. The second metal-binding site of 70 kDa heat-shock protein is essential for ADP binding, ATP hydrolysis and ATP synthesis. Biochem J. 2004;378:793-9 pubmed
    ..The first metal-binding site, a catalytic centre, is essential for ATP binding and the second site for ADP binding in the reactions of ATP hydrolysis and ATP synthesis. ..
  5. Nagahama M, Yamaguchi A, Hagiyama T, Ohkubo N, Kobayashi K, Sakurai J. Binding and internalization of Clostridium perfringens iota-toxin in lipid rafts. Infect Immun. 2004;72:3267-75 pubmed
    ..Surface plasmon resonance analysis revealed that Ia binds to the oligomer of Ib. We conclude that Ib binds to a receptor in membranes and then moves to rafts and that Ia bound to the oligomer of Ib formed in the rafts is internalized. ..
  6. Tsuji A, Kanie H, Makise H, Yuasa K, Nagahama M, Matsuda Y. Engineering of alpha1-antitrypsin variants selective for subtilisin-like proprotein convertases PACE4 and PC6: importance of the P2' residue in stable complex formation of the serpin with proprotein convertase. Protein Eng Des Sel. 2007;20:163-70 pubmed
    ..This is the first report of a highly selective protein-based inhibitor of PACE4 and PC6. This inhibitor will be useful in delineating the roles of PACE4 and PC6 localized in the extracellular matrix. ..
  7. Ohkura K, Kawaguchi Y, Tatematsu Y, Uto Y, Hori H. An Antitumor 2-Hydroxyarylidene-4-cyclopentene-1,3-Dione as a Protein Tyrosine Kinase Inhibitor: Interaction Between TX-1123 Derivatives and Src Kinase. Anticancer Res. 2016;36:3645-9 pubmed
    ..2 ?M), and fit into the pocket of the Src-K molecule as well as c-AMP did. The binding profiles of TX-1123 derivatives differed from each other, while their Src-K inhibitory activities were affected by their fit in the Src-K molecule. ..
  8. Naito E, Ito M, Yokota I, Saijo T, Matsuda J, Ogawa Y, et al. Thiamine-responsive pyruvate dehydrogenase deficiency in two patients caused by a point mutation (F205L and L216F) within the thiamine pyrophosphate binding region. Biochim Biophys Acta. 2002;1588:79-84 pubmed
    ..The DNA sequence of these two male patients' X-linked E1alpha subunit revealed a point mutation (F205L and L216F) within the TPP-binding region in exon 7...
  9. Nagamune H, Ohkura K, Sukeno A, Cowan G, Mitchell T, Ito W, et al. The human-specific action of intermedilysin, a homolog of streptolysin O, is dictated by domain 4 of the protein. Microbiol Immunol. 2004;48:677-92 pubmed

More Information


  1. Ueda K, Yoshihara M, Nakao M, Tanaka T, Sano S, Fukuzawa K, et al. Evaluation of inhibitory actions of flavonols and related substances on lysophospholipase d activity of serum autotaxin by a convenient assay using a chromogenic substrate. J Agric Food Chem. 2010;58:6053-63 pubmed publisher
  2. Kato Y, Fukui K, Suzuki K. Mechanism of a Mutation in Non-Structural Protein 1 Inducing High Pathogenicity of Avian Influenza Virus H5N1. Protein Pept Lett. 2016;23:372-8 pubmed
    ..Our results suggest that the single amino acid replacement induces a minor, but global structural change leading to the loss of function of NS1 thereby the change in the degree of pathogenicity. ..
  3. Maita N, Tsukimura T, Taniguchi T, Saito S, Ohno K, Taniguchi H, et al. Human ?-L-iduronidase uses its own N-glycan as a substrate-binding and catalytic module. Proc Natl Acad Sci U S A. 2013;110:14628-33 pubmed publisher
    ..The kinetics of native and deglycosylated hIDUA suggested that the N-glycan is also involved in catalytic processes. Our study demonstrates a previously unrecognized function of N-glycans. ..
  4. Fujiwara K, Hosaka H, Matsuda M, Okamura Ikeda K, Motokawa Y, Suzuki M, et al. Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP. J Mol Biol. 2007;371:222-34 pubmed
    ..We further demonstrate that bLT in mitochondria also contains endogenous lipoylmononucleotide, being ready for the lipoylation of apoproteins. ..
  5. Sakuraba H, Tsuge H, Yoneda K, Katunuma N, Ohshima T. Crystal structure of the NAD biosynthetic enzyme quinolinate synthase. J Biol Chem. 2005;280:26645-8 pubmed
    ..The model of the catalytic state during the first condensation step of the quinolinate synthase reaction indicates that the elimination of inorganic phosphate from dihydroxyacetone phosphate may precede the condensation reaction...
  6. Ohigashi I, Yamasaki Y, Hirashima T, Takahama Y. Identification of the transgenic integration site in immunodeficient tg?26 human CD3? transgenic mice. PLoS ONE. 2010;5:e14391 pubmed publisher
    ..However, none of the genes in this region were abrogated. These results suggest that the severe immunodeficiency seen in tg?26 mice is not due to gene disruption resulting from transgenic integration. ..
  7. Yamashita T, Kamada K, Hatcho K, Adachi A, Nomaguchi M. Identification of amino acid residues in HIV-1 Vif critical for binding and exclusion of APOBEC3G/F. Microbes Infect. 2008;10:1142-9 pubmed publisher
    ..Our results here have indicated that at least two distinct regions in the N-terminal half of HIV-1 Vif are critical for binding and exclusion of A3G/F. ..
  8. Kihira Y, Iwahashi A, Majima E, Terada H, Shinohara Y. Twisting of the second transmembrane alpha-helix of the mitochondrial ADP/ATP carrier during the transition between two carrier conformational states. Biochemistry. 2004;43:15204-9 pubmed
    ..On the basis of the results, the roles of TM2 in the transport function of AAC were discussed. ..
  9. Tsuchida K, Arai K, Kuramoto Y, Yamakawa N, Hasegawa Y, Sugino H. Identification and characterization of a novel follistatin-like protein as a binding protein for the TGF-beta family. J Biol Chem. 2000;275:40788-96 pubmed
    ..Our finding implies that cellular signaling by activin and BMPs is tightly regulated by multiple members of the follistatin family. ..
  10. Tashiro K, Tsunematsu T, Okubo H, Ohta T, Sano E, Yamauchi E, et al. GAREM, a novel adaptor protein for growth factor receptor-bound protein 2, contributes to cellular transformation through the activation of extracellular signal-regulated kinase signaling. J Biol Chem. 2009;284:20206-14 pubmed publisher
    ..Together, these findings suggest that GAREM plays a key role in the ligand-mediated signaling pathway of the EGF receptor and the tumorigenesis of cells. ..
  11. Kano S, Nishida K, Kurebe H, Nishiyama C, Kita K, Akaike Y, et al. Oxidative stress-inducible truncated serine/arginine-rich splicing factor 3 regulates interleukin-8 production in human colon cancer cells. Am J Physiol Cell Physiol. 2014;306:C250-62 pubmed publisher
    ..Our results suggest that SRSF3-TR may function as a positive regulator of oxidative stress-initiated inflammatory responses in colon cancer cells. ..
  12. Shamsul Alam M. Identification of important regulatory region of Th-POK. J Med Invest. 2010;57:219-23 pubmed
    ..These data suggest that the 22 bp element might positively regulate Th-POK expression through Erk-SAP-1 signaling. ..
  13. Ohkura K, Tatematsu Y, Kawaguchi Y, Uto Y, Hori H. Interactive Analysis of TX-1123 with Cyclo-oxygenase: Design of COX2 Selective TX Analogs. Anticancer Res. 2017;37:3849-3854 pubmed
    ..The TX-1123-binding pocket of COX2 differs from that of the COX2-selective celecoxib-binding pocket. TX-1123 exhibited a different COX2-interactive mechanism from that of celecoxib. ..
  14. Yamamoto H, Miyamoto K, Li B, Taketani Y, Kitano M, Inoue Y, et al. The caudal-related homeodomain protein Cdx-2 regulates vitamin D receptor gene expression in the small intestine. J Bone Miner Res. 1999;14:240-7 pubmed
    ..These findings suggest that Cdx-2 plays an important role in the intestine-specific transcription of the hVDR gene. ..
  15. Imagawa T, Iino H, Kanagawa M, Ebihara A, Kuramitsu S, Tsuge H. Crystal structure of the YdjC-family protein TTHB029 from Thermus thermophilus HB8: structural relationship with peptidoglycan N-acetylglucosamine deacetylase. Biochem Biophys Res Commun. 2008;367:535-41 pubmed publisher
    ..Moreover, these important metal-binding residues and the residues of the presumed active site are fully conserved in YdjC-family protein. ..
  16. Sakuraba H, Yoneda K, Yoshihara K, Satoh K, Kawakami R, Uto Y, et al. Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-ribose-5-phosphate aldolase. Appl Environ Microbiol. 2007;73:7427-34 pubmed
    ..This promotes the formation of the unique dimeric structure and strengthens the hydrophobic intersubunit interactions. These structural features are considered responsible for the extremely high stability of the hyperthermophilic DERAs. ..
  17. Yuasa K, Suzue K, Nagahama M, Matsuda Y, Tsuji A. Transcriptional regulation of subtilisin-like proprotein convertase PACE4 by E2F: possible role of E2F-mediated upregulation of PACE4 in tumor progression. Gene. 2007;402:103-10 pubmed
    ..Other E2F members, E2F2 and E2F3, also activated PACE4 expression, as in the case of E2F1. These results indicate a novel mechanism for E2F family-mediated promotion of carcinoma invasiveness through PACE4. ..
  18. Tanaka H, Yoshida K, Okamura H, Morimoto H, Nagata T, Haneji T. Calyculin A induces apoptosis and stimulates phosphorylation of p65NF-kappaB in human osteoblastic osteosarcoma MG63 cells. Int J Oncol. 2007;31:389-96 pubmed
  19. Okamura Ikeda K, Hosaka H, Yoshimura M, Yamashita E, Toma S, Nakagawa A, et al. Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia. J Mol Biol. 2005;351:1146-59 pubmed
    ..A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde...
  20. Bhuiya M, Sakuraba H, Ohshima T, Imagawa T, Katunuma N, Tsuge H. The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum. J Mol Biol. 2005;345:325-37 pubmed
    ..This indicates that the major molecular strategy for high thermostability of the GluDHs may be different for each hyperthermophile. ..
  21. Yasui N, Mori T, Morito D, Matsushita O, Kourai H, Nagata K, et al. Dual-site recognition of different extracellular matrix components by anti-angiogenic/neurotrophic serpin, PEDF. Biochemistry. 2003;42:3160-7 pubmed
    ..These results indicate that PEDF possesses dual binding sites for different ECM components, and this unique localization of ECM-binding sites implies that the binding to ECM components could regulate PEDF activities. ..
  22. Kuzuhara T, Kise D, Yoshida H, Horita T, Murazaki Y, Utsunomiya H, et al. Crystallization and X-ray diffraction analysis of the RNA primer/promoter-binding domain of influenza A virus RNA-dependent RNA polymerase PB2. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:144-6 pubmed publisher
    ..The SeMet-derivative crystals were found to belong to the same space group, with unit-cell parameters a = b = 52.6, c = 156.4 A. Attempts are being made to solve the structure by multi-wavelength anomalous dispersion phasing. ..
  23. Nakatsuji H, Nishimura N, Yamamura R, Kanayama H, Sasaki T. Involvement of actinin-4 in the recruitment of JRAB/MICAL-L2 to cell-cell junctions and the formation of functional tight junctions. Mol Cell Biol. 2008;28:3324-35 pubmed publisher
    ..These results indicate that actinin-4 is involved in recruiting JRAB/MICAL-L2 to cell-cell junctions and forming functional TJs. ..
  24. Imagawa T, Tsurumura T, Sugimoto Y, Aki K, Ishidoh K, Kuramitsu S, et al. Structural basis of free reduced flavin generation by flavin reductase from Thermus thermophilus HB8. J Biol Chem. 2011;286:44078-85 pubmed publisher
    ..Our findings suggest that the C-terminal region of TTHA0420 may regulate the alternative binding of NADH and substrate flavin to the enzyme. ..
  25. Fujiwara K, Toma S, Okamura Ikeda K, Motokawa Y, Nakagawa A, Taniguchi H. Crystal structure of lipoate-protein ligase A from Escherichia coli. Determination of the lipoic acid-binding site. J Biol Chem. 2005;280:33645-51 pubmed
    ..No large conformational change was observed in the main chain structure upon the binding of lipoic acid. ..
  26. Tanaka K, Kato A, Angelocci C, Watanabe M, Kato Y. A potential molecular pathogenesis of cardiac/laterality defects in Oculo-Facio-Cardio-Dental syndrome. Dev Biol. 2014;387:28-36 pubmed publisher
    ..The study presented here uncovers the regulatory mechanism of Pitx2 gene transcription which may contribute to an understanding of pathogenesis of OFCD syndrome. ..
  27. Okamura Ikeda K, Fujiwara K, Motokawa Y. Identification of the folate binding sites on the Escherichia coli T-protein of the glycine cleavage system. J Biol Chem. 1999;274:17471-7 pubmed