Publications


    2011

  1. Nakayama H, Takahashi N, Isobe T. "Informatics for mass spectrometry-based RNA analysis." Mass Spectrom Rev. 2011 Nov-Dec;30(6):1000-12. doi: 10.1002/mas.20325. Epub 2011 Feb 16.[pubmed]
  2. Takahashi H, Suzuki T, Shirai A, Matsuyama A, Dohmae N, Yoshida M. "Mitochondrial localization of fission yeast manganese superoxide dismutase is required for its lysine acetylation and for cellular stress resistance and respiratory growth." Biochem Biophys Res Commun. 2011 Mar 4;406(1):42-6. Epub 2011 Feb 2.[pubmed]
  3. Itoh K, Izumi A, Mori T, Dohmae N, Yui R, Maeda-Sano K, Shirai Y, Kanaoka MM, Kuroiwa T, Higashiyama T, Sugita M, Murakami-Murofushi K, Kawano S, Sasaki N. "DNA packaging proteins Glom and Glom2 coordinately organize the mitochondrial nucleoid of Physarum polycephalum." Mitochondrion. 2011 Jul;11(4):575-86. Epub 2011 Mar 23.[pubmed]
  4. Nagamine T, Abe A, Suzuki T, Dohmae N, Matsumoto S. "Co-expression of four baculovirus proteins, IE1, LEF3, P143, and PP31, elicits a cellular chromatin-containing reticulate structure in the nuclei of uninfected cells." Virology. 2011 Aug 15;417(1):188-95. Epub 2011 Jun 24.[pubmed]
  5. Echizen Y, Tsukazaki T, Dohmae N, Ishitani R, Nureki O. "Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, from Thermus thermophilus." Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Nov 1;67(Pt 11):1367-70. Epub 2011 Oct 27.[pubmed]
  6. Takahashi K, Suzuki T, Nishii W, Kubota K, Shibata C, Isobe T, Dohmae N. "A cysteine endopeptidase ("dionain") is involved in the digestive fluid of Dionaea muscipula (Venus's fly-trap)." Biosci Biotechnol Biochem. 2011;75(2):346-8. Epub 2011 Feb 7.[pubmed]
  7. Nishimasu H, Okudaira S, Hama K, Mihara E, Dohmae N, Inoue A, Ishitani R, Takagi J, Aoki J, Nureki O. "Crystal structure of autotaxin and insight into GPCR activation by lipid mediators." Nat Struct Mol Biol. 2011 Feb;18(2):205-12. Epub 2011 Jan 16.[pubmed]
  8. Asanuma M, Kurokawa K, Ichikawa R, Ryu KH, Chae JH, Dohmae N, Lee BL, Nakayama H. "Structural evidence of α-aminoacylated lipoproteins of Staphylococcus aureus." FEBS J. 2011 Mar;278(5):716-28. doi: 10.1111/j.1742-4658.2010.07990.x. Epub 2011 Jan 12.[pubmed]
  9. Cho HS, Suzuki T, Dohmae N, Hayami S, Unoki M, Yoshimatsu M, Toyokawa G, Takawa M, Chen T, Kurash JK, Field HI, Ponder BA, Nakamura Y, Hamamoto R. "Demethylation of RB regulator MYPT1 by histone demethylase LSD1 promotes cell cycle progression in cancer cells." Cancer Res. 2011 Feb 1;71(3):655-60. Epub 2010 Nov 29.[pubmed]
  10. Ohnishi A, Hull JJ, Kaji M, Hashimoto K, Lee JM, Tsuneizumi K, Suzuki T, Dohmae N, Matsumoto S. "Hormone signaling linked to silkmoth sex pheromone biosynthesis involves Ca2+/calmodulin-dependent protein kinase II-mediated phosphorylation of the insect PAT family protein Bombyx mori lipid storage droplet protein-1 (BmLsd1)." J Biol Chem. 2011 Jul 8;286(27):24101-12. Epub 2011 May 15.[pubmed]
  11. Masuda A, Dohmae N. "Amino acid analysis of sub-picomolar amounts of proteins by precolumn fluorescence derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate." Biosci Trends. 2011 Dec;5(6):231-8.[pubmed]

    12. 2010

  12. Yu Y, Park JW, Kwon HM, Hwang HO, Jang IH, Masuda A, Kurokawa K, Nakayama H, Lee WJ, Dohmae N, Zhang J, Lee BL. "Diversity of innate immune recognition mechanism for bacterial polymeric meso-diaminopimelic acid-type peptidoglycan in insects." J Biol Chem. 2010 Oct 22;285(43):32937-45. Epub 2010 Aug 11.[pubmed]
  13. Iwai M, Suzuki T, Kamiyama A, Sakurai I, Dohmae N, Inoue Y, Ikeuchi M. "The PsbK subunit is required for the stable assembly and stability of other small subunits in the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1." Plant Cell Physiol. 2010 Apr;51(4):554-60. Epub 2010 Mar 1.[pubmed]
  14. Suzuki MG, Imanishi S, Dohmae N, Asanuma M, Matsumoto S. "Identification of a male-specific RNA binding protein that regulates sex-specific splicing of Bmdsx by increasing RNA binding activity of BmPSI." Mol Cell Biol. 2010 Dec;30(24):5776-86. Epub 2010 Oct 18.[pubmed]
  15. Sato Y, Shimizu S, Ohtaki A, Noguchi K, Miyatake H, Dohmae N, Sasaki S, Odaka M, Yohda M. "Crystal structures of the lumazine protein from Photobacterium kishitanii in complexes with the authentic chromophore, 6,7-dimethyl- 8-(1'-D-ribityl) lumazine, and its analogues, riboflavin and flavin mononucleotide, at high resolution." J Bacteriol. 2010 Jan;192(1):127-33.[pubmed]
  16. Nagao R, Suzuki T, Okumura A, Niikura A, Iwai M, Dohmae N, Tomo T, Shen JR, Ikeuchi M, Enami I. "Topological analysis of the extrinsic PsbO, PsbP and PsbQ proteins in a green algal PSII complex by cross-linking with a water-soluble carbodiimide." Plant Cell Physiol. 2010 May;51(5):718-27. Epub 2010 Apr 7.[pubmed]
  17. Obata Y, Fukumoto Y, Nakayama Y, Kuga T, Dohmae N, Yamaguchi N. "The Lyn kinase C-lobe mediates Golgi export of Lyn through conformation-dependent ACSL3 association." J Cell Sci. 2010 Aug 1;123(Pt 15):2649-62. Epub 2010 Jul 6.[pubmed]
  18. Masuda A, Dohmae N. "Automated Protein Hydrolysis Delivering Sample to a Solid Acid Catalyst for Amino Acid Analysis." Anal Chem. 2010 Oct;82(21) :8939-8945. Epub 2010 Oct 5.[pubmed]
  19. Nagao R, Moriguchi A, Tomo T, Niikura A, Nakajima S, Suzuki T, Okumura A, Iwai M, Shen JR, Ikeuchi M, Enami I. "Binding and functional properties of five extrinsic proteins in oxygen-evolving photosystem II from a marine centric diatom, Chaetoceros gracilis." J Biol Chem. 2010 Sep 17;285(38):29191-9. Epub 2010 Jul 14.[pubmed]
  20. Taoka M, Ikumi M, Nakayama H, Masaki S, Matsuda R, Nobe Y, Yamauchi Y, Takeda J, Takahashi N, Isobe T. "In-gel digestion for mass spectrometric characterization of RNA from fluorescently stained polyacrylamide gels." Anal Chem. 2010 Sep 15;82(18):7795-803.[pubmed]
  21. Kodama K, Nakayama H, Sakamoto K, Fukuzawa S, Kigawa T, Yabuki T, Kitabatake M, Takio K, Yokoyama S. "Site-specific incorporation of 4-iodo-L-phenylalanine through opal suppression." J Biochem. 2010 Aug;148(2):179-87. Epub 2010 May 21.[pubmed]
  22. Saito K, Kagawa W, Suzuki T, Suzuki H, Yokoyama S, Saitoh H, Tashiro S, Dohmae N, Kurumizaka H. "The putative nuclear localization signal of the human RAD52 protein is a potential sumoylation site." J Biochem. 2010 Jun;147(6):833-42. Epub 2010 Feb 27.[pubmed]
  23. Nakanishi T, Goto C, Kobayashi M, Kang W, Suzuki T, Dohmae N, Matsumoto S, Shimada T, Katsuma S. "Comparative studies of lepidopteran baculovirus-specific protein FP25K: development of a novel Bombyx mori nucleopolyhedrovirus-based vector with a modified fp25K gene." J Virol. 2010 May;84(10):5191-200. Epub 2010 Mar 10.[pubmed]
  24. Sahlan M, Zako T, Tai PT, Ohtaki A, Noguchi K, Maeda M, Miyatake H, Dohmae N, Yohda M. "Thermodynamic characterization of the interaction between prefoldin and group II chaperonin." J Mol Biol. 2010 Jun 18;399(4):628-36. Epub 2010 Apr 29.[pubmed]
  25. Ohtaki A, Murata K, Sato Y, Noguchi K, Miyatake H, Dohmae N, Yamada K, Yohda M, Odaka M. "Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition." Biochim Biophys Acta. 2010 Jan;1804(1):184-92. Epub 2009 Oct 9.[pubmed]
  26. Yoshida M, Higashi K, Jin L, Machi Y, Suzuki T, Masuda A, Dohmae N, Suganami A, Tamura Y, Nishimura K, Toida T, Tomitori H, Kashiwagi K, Igarashi K. "Identification of acrolein-conjugated protein in plasma of patients with brain infarction." Biochem Biophys Res Commun. 2010 Jan 8;391(2):1234-9. Epub 2009 Dec 16.[pubmed]
  27. Nagao R, Tomo T, Noguchi E, Nakajima S, Suzuki T, Okumura A, Kashino Y, Mimuro M, Ikeuchi M, Enami I. "Purification and characterization of a stable oxygen-evolving Photosystem II complex from a marine centric diatom, Chaetoceros gracilis." Biochim Biophys Acta. 2010 Feb;1797(2):160-6. Epub 2009 Sep 23.[pubmed]

    28. 2009

  28. Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T. "Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data." Nucleic Acids Res. 2009 Apr;37(6):e47. Epub 2009 Mar 6.[pubmed]
  29. Taoka M, Yamauchi Y, Nobe Y, Masaki S, Nakayama H, Ishikawa H, Takahashi N, Isobe T. "An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes." Nucleic Acids Res. 2009 Nov;37(21):e140.[pubmed]
  30. Kurokawa K, Lee H, Roh KB, Asanuma M, Kim YS, Nakayama H, Shiratsuchi A, Choi Y, Takeuchi O, Kang HJ, Dohmae N, Nakanishi Y, Akira S, Sekimizu K, Lee BL. "The Triacylated ATP Binding Cluster Transporter Substrate-binding Lipoprotein of Staphylococcus aureus Functions as a Native Ligand for Toll-like Receptor 2." J Biol Chem. 2009 Mar 27;284(13):8406-11. Epub 2009 Jan 12.[pubmed]
  31. Kametani F, Nonaka T, Suzuki T, Arai T, Dohmae N, Akiyama H, Hasegawa M. "Identification of casein kinase-1 phosphorylation sites on TDP-43." Biochem Biophys Res Commun. 2009 May 1;382(2):405-9. Epub 2009 Mar 13.[pubmed]
  32. Nishimura K, Okudaira H, Ochiai E, Higashi K, Kaneko M, Ishii I, Nishimura T, Dohmae N, Kashiwagi K, Igarashi K. "Identification of proteins whose synthesis is preferentially enhanced by polyamines at the level of translation in mammalian cells." Int J Biochem Cell Biol. 2009 Nov;41(11):2251-61. Epub 2009 May 7.[pubmed]
  33. Yonashiro R, Sugiura A, Miyachi M, Fukuda T, Matsushita N, Inatome R, Ogata Y, Suzuki T, Dohmae N, Yanagi S. "Mitochondrial ubiquitin ligase MITOL ubiquitinates mutant SOD1 and attenuates mutant SOD1-induced reactive oxygen species generation." Mol Biol Cell. 2009 Nov;20(21):4524-30. Epub 2009 Sep 9.[pubmed]
  34. Kuraishi T, Nakagawa Y, Nagaosa K, Hashimoto Y, Ishimoto T, Moki T, Fujita Y, Nakayama H, Dohmae N, Shiratsuchi A, Yamamoto N, Ueda K, Yamaguchi M, Awasaki T, Nakanishi Y. "Pretaporter, a Drosophila protein serving as a ligand for Draper in the phagocytosis of apoptotic cells." EMBO J. 2009 Dec 16;28(24):3868-78.[pubmed]
  35. Okumura A, Suzuki T, Dohmae N, Okabe T, Hashimoto Y, Nakazato K, Ohno H, Miyazaki Y, Yamagoe S. "Identification and assignment of three disulfide bonds in mammalian leukocyte cell-derived chemotaxin 2 by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry." Biosci Trends. 2009 Aug;3(4):139-43.[pubmed]
  36. Yatagai F, Sugasawa K, Enomoto S, Honma M. "An approach to estimate radioadaptation from DSB repair efficiency." J Radiat Res. 2009 Sep;50(5):407-13. Epub 2009 Aug 13.[pubmed]
  37. Arakawa T, Kawano Y, Katayama Y, Nakayama H, Dohmae N, Yohda M, Odaka M. "Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification." J Am Chem Soc. 2009 Oct 21;131(41):14838-43.[pubmed]
  38. Iida T, Moteki Y, Nakamura K, Taguchi K, Otagiri M, Asanuma M, Dohmae N, Usami R, Kudo T. "Functional expression of three Rieske non-heme iron oxygenases derived from actinomycetes in Rhodococcus species for investigation of their degradation capabilities of dibenzofuran and chlorinated dioxins." Biosci Biotechnol Biochem. 2009 Apr 23;73(4):822-7. Epub 2009 Apr 7.[pubmed]

    39. 2008

  39. Enami I, Okumura A, Nagao R, Suzuki T, Iwai M, Shen JR. "Structures and functions of the extrinsic proteins of photosystem II from different species." Photosynth Res. 2008 Oct-Dec;98(1-3):349-63. Epub 2008 Aug 21.[pubmed]
  40. Okumura A, Nagao R, Suzuki T, Yamagoe S, Iwai M, Nakazato K, Enami I. "A novel protein in Photosystem II of a diatom Chaetoceros gracilis is one of the extrinsic proteins located on lumenal side and directly associates with PSII core components." Biochim Biophys Acta. 2008 Dec;1777(12):1545-51. Epub 2008 Sep 18.[pubmed]
  41. Yatagai F, Umebayashi Y, Honma M, Sugasawa K, Takayama Y, Hanaoka F. "Mutagenic radioadaptation in a human lymphoblastoid cell line." Mutat Res. 2008 Feb 1;638(1-2):48-55. Epub 2007 Sep 1.[pubmed]
  42. Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K, Nureki O. "Conformational transition of Sec machinery inferred from bacterial SecYE structures." Nature. 2008 Oct 16;455(7215):988-91.[pubmed]
  43. Taniguchi K, Murata K, Murakami Y, Takahashi S, Nakamura T, Hashimoto K, Koshino H, Dohmae N, Yohda M, Hirose T, Maeda M, Odaka M. "Novel catalytic activity of nitrile hydratase from Rhodococcus sp. N771." J Biosci Bioeng. 2008 Aug;106(2):174-9.[pubmed]
  44. Ishitani R, Sugita Y, Dohmae N, Furuya N, Hattori M, Nureki O. "Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study." Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15393-8. Epub 2008 Oct 1.[pubmed]
  45. Tomo T, Kato Y, Suzuki T, Akimoto S, Okubo T, Noguchi T, Hasegawa K, Tsuchiya T, Tanaka K, Fukuya M, Dohmae N, Watanabe T, Mimuro M. "Characterization of highly purified photosystem I complexes from the chlorophyll d-dominated cyanobacterium Acaryochloris marina MBIC 11017." J Biol Chem. 2008 Jun 27;283(26):18198-209. Epub 2008 May 5.[pubmed]
  46. Menon S, Tsuge T, Dohmae N, Takio K, Wei N. "Association of SAP130/SF3b-3 with Cullin-RING ubiquitin ligase complexes and its regulation by the COP9 signalosome." BMC Biochem. 2008 Jan 3;9:1.[pubmed]
  47. Yokoyama K, Nakagawa M, Satoh M, Saitoh S, Dohmae N, Harada A, Satoh N, Karasawa K, Takio K, Yanagida M, Inoue K. "Expression of a novel 90-kDa protein, Lsd90, involved in the metabolism of very long-chain fatty acid-containing phospholipids in a mitosis-defective fission yeast mutant." J Biochem. 2008 Mar;143(3):369-75. Epub 2007 Dec 13.[pubmed]
  48. Fujibayashi A, Taguchi T, Misaki R, Ohtani M, Dohmae N, Takio K, Yamada M, Gu J, Yamakami M, Fukuda M, Waguri S, Uchiyama Y, Yoshimori T, Sekiguchi K. "Human RME-8 is involved in membrane trafficking through early endosomes." Cell Struct Funct. 2008;33(1):35-50. Epub 2008 Feb 6.[pubmed]
  49. Hayashi M, Tamura Y, Dohmae N, Kojima S, Shimonaka M. "Plasminogen N-terminal activation peptide modulates the activity of angiostatin-related peptides on endothelial cell proliferation and migration." Biochem Biophys Res Commun. 2008 May 2;369(2):635-40. Epub 2008 Feb 21.[pubmed]
  50. Suzuki MG, Imanishi S, Dohmae N, Nishimura T, Shimada T, Matsumoto S. "Establishment of a novel in vivo sex-specific splicing assay system to identify a trans-acting factor that negatively regulates splicing of Bombyx mori dsx female exons." Mol Cell Biol. 2008 Jan;28(1):333-43. Epub 2007 Oct 29.[pubmed]

    51. 2007

  51. Noji N, Nakamura T, Kitahata N, Taguchi K, Kudo T, Yoshida S, Tsujimoto M, Sugiyama T, Asami T. "Simple and sensitive method for pyrroloquinoline quinone (PQQ) analysis in various foods using liquid chromatography/electrospray-ionization tandem mass spectrometry." J Agric Food Chem. 2007 Sep 5;55(18):7258-63. Epub 2007 Aug 9.[pubmed]
  52. Sahara N, Maeda S, Murayama M, Suzuki T, Dohmae N, Yen SH, Takashima A. "Assembly of two distinct dimers and higher-order oligomers from full-length tau." Eur J Neurosci. 2007 May;25(10):3020-9.[pubmed]
  53. Nagao R, Ishii A, Tada O, Suzuki T, Dohmae N, Okumura A, Iwai M, Takahashi T, Kashino Y, Enami I. "Isolation and characterization of oxygen-evolving thylakoid membranes and photosystem II particles from a marine diatom Chaetoceros gracilis." Biochim Biophys Acta. 2007 Dec;1767(12):1353-62. Epub 2007 Oct 23.[pubmed]
  54. Okumura A, Sano M, Suzuki T, Tanaka H, Nagao R, Nakazato K, Iwai M, Adachi H, Shen JR, Enami I. "Aromatic structure of tyrosine-92 in the extrinsic PsbU protein of red algal photosystem II is important for its functioning." FEBS Lett. 2007 Nov 13;581(27):5255-8. Epub 2007 Oct 16.[pubmed]
  55. Iwai M, Suzuki T, Dohmae N, Inoue Y, Ikeuchi M. "Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1." Plant Cell Physiol. 2007 Dec;48(12):1758-63. Epub 2007 Oct 28.[pubmed]
  56. Masuda A, Baba T, Dohmae N, Yamamura M, Wada H, Ushida K. "Mucin (qniumucin), a glycoprotein from jellyfish, and determination of its main chain structure." J Nat Prod. 2007 Jul;70(7):1089-92. Epub 2007 Jun 14.[pubmed]
  57. Nakanishi K, Dohmae N, Morishima N. "Endoplasmic reticulum stress increases myofiber formation in vitro." FASEB J. 2007 Sep;21(11):2994-3003. Epub 2007 Apr 13.[pubmed]
  58. Linge A, Morishima N, Kasper M, Barth K. "Bleomycin induces caveolin-1 and -2 expression in epithelial lung cancer A549 cells." Anticancer Res. 2007 May-Jun;27(3A):1343-51.[pubmed]
  59. Kim SH, Miyatake H, Hisano T, Iwasaki W, Ebihara A, Miki K. "Crystallization and preliminary X-ray analysis of the oxygenase component (HpaB) of 4-hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus HB8." Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Jul 1;63(Pt 7):556-9. Epub 2007 Jun 11.[pubmed]
  60. Simizu S, Suzuki T, Muroi M, Lai NS, Takagi S, Dohmae N, Osada H. "Involvement of disulfide bond formation in the activation of heparanase." Cancer Res. 2007 Aug 15;67(16):7841-9.[pubmed]
  61. Pick E, Lau OS, Tsuge T, Menon S, Tong Y, Dohmae N, Plafker SM, Deng XW, Wei N. "Mammalian DET1 regulates Cul4A activity and forms stable complexes with E2 ubiquitin-conjugating enzymes." Mol Cell Biol. 2007 Jul;27(13):4708-19. Epub 2007 Apr 23.[pubmed]
  62. Torigoe H, Dohmae N, Hanaoka F, Furukawa A. "Mutational analyses of a single-stranded telomeric DNA binding domain of fission yeast pot1: conflict with X-ray crystallographic structure." Biosci Biotechnol Biochem. 2007 Feb;71(2):481-90. Epub 2007 Feb 7.[pubmed]
  63. Sato Y, Shirakawa R, Horiuchi H, Dohmae N, Fukai S, Nureki O. "Asymmetric coiled-coil structure with Guanine nucleotide exchange activity." Structure. 2007 Feb;15(2):245-52.[pubmed]
  64. Manya H, Suzuki T, Akasaka-Manya K, Ishida HK, Mizuno M, Suzuki Y, Inazu T, Dohmae N, Endo T. "Regulation of mammalian protein O-mannosylation: preferential amino acid sequence for O-mannose modification." J Biol Chem. 2007 Jul 13;282(28):20200-6. Epub 2007 May 14.[pubmed]
  65. Umehara M, Ogita S, Sasamoto H, Koshino H, Nakamura Takemichi, Asami Tadao, Yoshida Shigeo, Kamada H, "Identification of a factor that complementarily inhibits somatic embryogenesis with vanillyl benzyl ether in Japanese larch" In Vitro Cellular Developmental Biology Plant 2007 43(3):203-208. [pdf]
  66. Hongo Yayoi, Nakamura Takemichi, Sato Akihiro, "Electron capture dissociation of triantennary complex-type N-glycosylated peptides: a case of suppressed peptide backbone cleavage" Journal of the Mass Spectrometry Society of Japan 2007 55(2):77-82 [pdf]
  67. Hongo Yayoi, Sato Akihiro, Nakamura Takemichi, "Factors governing peptide backbone cleavages in electron capture dissociation of triantennary complex-type N-glycosylated peptide" Journal of the Mass Spectrometry Society of Japan 2007 55(4):279-285 [pdf]

    68. 2006

  68. Kodama K, Fukuzawa S, Sakamoto K, Nakayama H, Kigawa T, Yabuki T, Matsuda N, Shirouzu M, Takio K, Tachibana K, Yokoyama S. "A new protein engineering approach combining chemistry and biology, part I; site-specific incorporation of 4-iodo-L-phenylalanine in vitro by using misacylated suppressor tRNAPhe." Chembiochem. 2006 Oct;7(10):1577-81.[pubmed]
  69. Masuda M, Dohmae N, Nonaka T, Oikawa T, Hisanaga S, Goedert M, Hasegawa M. "Cysteine misincorporation in bacterially expressed human alpha-synuclein." FEBS Lett. 2006 Mar 20;580(7):1775-9. Epub 2006 Feb 24.[pubmed]
  70. Kakuda N, Funamoto S, Yagishita S, Takami M, Osawa S, Dohmae N, Ihara Y. "Equimolar production of amyloid beta-protein and amyloid precursor protein intracellular domain from beta-carboxyl-terminal fragment by gamma-secretase." J Biol Chem. 2006 May 26;281(21):14776-86. Epub 2006 Apr 4.[pubmed]
  71. Takayasu S, Sakurai T, Iwasaki S, Teranishi H, Yamanaka A, Williams SC, Iguchi H, Kawasawa YI, Ikeda Y, Sakakibara I, Ohno K, Ioka RX, Murakami S, Dohmae N, Xie J, Suda T, Motoike T, Ohuchi T, Yanagisawa M, Sakai J. "A neuropeptide ligand of the G protein-coupled receptor GPR103 regulates feeding, behavioral arousal, and blood pressure in mice." Proc Natl Acad Sci U S A. 2006 May 9;103(19):7438-43. Epub 2006 Apr 28.[pubmed]
  72. Kaku H, Nishizawa Y, Ishii-Minami N, Akimoto-Tomiyama C, Dohmae N, Takio K, Minami E, Shibuya N. "Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor." Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):11086-91. Epub 2006 Jul 7.[pubmed]
  73. Dreanno C, Matsumura K, Dohmae N, Takio K, Hirota H, Kirby RR, Clare AS. "An alpha2-macroglobulin-like protein is the cue to gregarious settlement of the barnacle Balanus amphitrite." Proc Natl Acad Sci U S A. 2006 Sep 26;103(39):14396-401. Epub 2006 Sep 18.[pubmed]
  74. Ito Y, Nakanomyo I, Motose H, Iwamoto K, Sawa S, Dohmae N, Fukuda H. "Dodeca-CLE peptides as suppressors of plant stem cell differentiation." Science. 2006 Aug 11;313(5788):842-5.[pubmed]
  75. Takarada H, Kawano Y, Hashimoto K, Nakayama H, Ueda S, Yohda M, Kamiya N, Dohmae N, Maeda M, Odaka M. "Mutational study on alphaGln90 of Fe-type nitrile hydratase from Rhodococcus sp. N771." Biosci Biotechnol Biochem. 2006 Apr;70(4):881-9.[pubmed]
  76. Nagatsuka Y, Horibata Y, Yamazaki Y, Kinoshita M, Shinoda Y, Hashikawa T, Koshino H, Nakamura T, Hirabayashi Y. "Phosphatidylglucoside exists as a single molecular species with saturated fatty acyl chains in developing astroglial membranes." Biochemistry. 2006 Jul 25;45(29):8742-50.[pubmed]
  77. Katayama Y, Hashimoto K, Nakayama H, Mino H, Nojiri M, Ono TA, Nyunoya H, Yohda M, Takio K, Odaka M. "Thiocyanate hydrolase is a cobalt-containing metalloenzyme with a cysteine-sulfinic acid ligand." J Am Chem Soc. 2006 Jan 25;128(3):728-9.[pubmed]
  78. Kodama K, Fukuzawa S, Nakayama H, Kigawa T, Sakamoto K, Yabuki T, Matsuda N, Shirouzu M, Takio K, Tachibana K, Yokoyama S. "Regioselective carbon-carbon bond formation in proteins with palladium catalysis; new protein chemistry by organometallic chemistry." Chembiochem. 2006 Jan;7(1):134-9.[pubmed]
  79. Tomo Tatsuya, Suzuki Takehiro, Hirano Emi, Tsuchiya Tohru, Miyashita Hideaki, Dohmae Naoshi, Mimuro Mamoru, "Reversible absorption change of chlorophyll {\it d} in solutions" Chemical Physics Letters 2006 423:282-287 [link]

    80. 2005

  80. Nagumo Y, Kakeya H, Shoji M, Hayashi Y, Dohmae N, Osada H. "Epolactaene binds human Hsp60 Cys442 resulting in the inhibition of chaperone activity." Biochem J. 2005 May 1;387(Pt 3):835-40.[pubmed]
  81. Nakai Y, Shiratsuchi A, Manaka J, Nakayama H, Takio K, Zhang JT, Suganuma T, Nakanishi Y. "Externalization and recognition by macrophages of large subunit of eukaryotic translation initiation factor 3 in apoptotic cells." Exp Cell Res. 2005 Sep 10;309(1):137-48.[pubmed]
  82. Aoki K, Suzui N, Fujimaki S, Dohmae N, Yonekura-Sakakibara K, Fujiwara T, Hayashi H, Yamaya T, Sakakibara H. "Destination-selective long-distance movement of phloem proteins." Plant Cell. 2005 Jun;17(6):1801-14. Epub 2005 Apr 29.[pubmed]
  83. Nakanishi K, Sudo T, Morishima N. "Endoplasmic reticulum stress signaling transmitted by ATF6 mediates apoptosis during muscle development." J Cell Biol. 2005 May 23;169(4):555-60. Epub 2005 May 16.[pubmed]
  84. Morishima N. "Control of cell fate by Hsp70: more than an evanescent meeting." J Biochem. 2005 Apr;137(4):449-53.[pubmed]

    85. 2004

  85. Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N, Isobe T. "Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins." Mol Cell Proteomics. 2004 Aug;3(8):780-7. Epub 2004 Apr 28.[pubmed]
  86. Iwata H, Kaibara M, Dohmae N, Takio K, Himeno R, Kawakami S. "Purification, identification, and characterization of elastase on erythrocyte membrane as factor IX-activating enzyme." Biochem Biophys Res Commun. 2004 Mar 26;316(1):65-70.[pubmed]
  87. Ishida M, Dohmae N, Shiro Y, Oku T, Iizuka T, Isogai Y. "Design and synthesis of de novo cytochromes c." Biochemistry. 2004 Aug 3;43(30):9823-33.[pubmed]
  88. Tomita T, Mizumachi Y, Chong K, Ogawa K, Konishi N, Sugawara-Tomita N, Dohmae N, Hashimoto Y, Takio K. "Protein sequence analysis, cloning, and expression of flammutoxin, a pore-forming cytolysin from Flammulina velutipes. Maturation of dimeric precursor to monomeric active form by carboxyl-terminal truncation." J Biol Chem. 2004 Dec 24;279(52):54161-72. Epub 2004 Oct 15.[pubmed]
  89. Watanabe A, Hong WK, Dohmae N, Takio K, Morishima-Kawashima M, Ihara Y. "Molecular aging of tau: disulfide-independent aggregation and non-enzymatic degradation in vitro and in vivo." J Neurochem. 2004 Sep;90(6):1302-11.[pubmed]
  90. Kanai Y, Dohmae N, Hirokawa N. "Kinesin transports RNA: isolation and characterization of an RNA-transporting granule." Neuron. 2004 Aug 19;43(4):513-25.[pubmed]
  91. Aihara H, Nakagawa T, Yasui K, Ohta T, Hirose S, Dhomae N, Takio K, Kaneko M, Takeshima Y, Muramatsu M, Ito T. "Nucleosomal histone kinase-1 phosphorylates H2A Thr 119 during mitosis in the early Drosophila embryo." Genes Dev. 2004 Apr 15;18(8):877-88. Epub 2004 Apr 12.[pubmed]
  92. Hirose H, Arasaki K, Dohmae N, Takio K, Hatsuzawa K, Nagahama M, Tani K, Yamamoto A, Tohyama M, Tagaya M. "Implication of ZW10 in membrane trafficking between the endoplasmic reticulum and Golgi." EMBO J. 2004 Mar 24;23(6):1267-78. Epub 2004 Mar 18.[pubmed]
  93. Tohri A, Dohmae N, Suzuki T, Ohta H, Inoue Y, Enami I. "Identification of domains on the extrinsic 23 kDa protein possibly involved in electrostatic interaction with the extrinsic 33 kDa protein in spinach photosystem II." Eur J Biochem. 2004 Mar;271(5):962-71.[pubmed]
  94. Usui T, Kazami S, Dohmae N, Mashimo Y, Kondo H, Tsuda M, Terasaki AG, Ohashi K, Kobayashi J, Osada H. "Amphidinolide h, a potent cytotoxic macrolide, covalently binds on actin subdomain 4 and stabilizes actin filament." Chem Biol. 2004 Sep;11(9):1269-77.[pubmed]
  95. Shibata M, Ishii J, Koizumi H, Shibata N, Dohmae N, Takio K, Adachi H, Tsujimoto M, Arai H. "Type F scavenger receptor SREC-I interacts with advillin, a member of the gelsolin/villin family, and induces neurite-like outgrowth." J Biol Chem. 2004 Sep 17;279(38):40084-90. Epub 2004 Jul 9.[pubmed]
  96. Nakamura T, Dohmae N, Takio K. "Characterization of a digested protein complex with quantitative aspects: an approach based on accurate mass chromatographic analysis with Fourier transform-ion cyclotron resonance mass spectrometry." Proteomics. 2004 Sep;4(9):2558-66.[pubmed]
  97. Usui T, Watanabe H, Nakayama H, Tada Y, Kanoh N, Kondoh M, Asao T, Takio K, Watanabe H, Nishikawa K, Kitahara T, Osada H. "The anticancer natural product pironetin selectively targets Lys352 of alpha-tubulin." Chem Biol. 2004 Jun;11(6):799-806.[pubmed]
  98. Kanki T, Nakayama H, Sasaki N, Takio K, Alam TI, Hamasaki N, Kang D. "Mitochondrial nucleoid and transcription factor A." Ann N Y Acad Sci. 2004 Apr;1011:61-8.[pubmed]
  99. Sengoku T, Nureki O, Dohmae N, Nakamura A, Yokoyama S. "Crystallization and preliminary X-ray analysis of the helicase domains of Vasa complexed with RNA and an ATP analogue." Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):320-2. Epub 2004 Jan 23.[pubmed]

    100. 2003

  100. Hoshino M, Dohmae N, Takio K, Kanazawa I, Nukina N. "Identification of a novel amino-terminal fragment of amyloid precursor protein in mouse neuroblastoma Neuro2a cell." Neurosci Lett. 2003 Dec 19;353(2):135-8.[pubmed]
  101. Sato T, Dohmae N, Qi Y, Kakuda N, Misonou H, Mitsumori R, Maruyama H, Koo EH, Haass C, Takio K, Morishima-Kawashima M, Ishiura S, Ihara Y. "Potential link between amyloid beta-protein 42 and C-terminal fragment gamma 49-99 of beta-amyloid precursor protein." J Biol Chem. 2003 Jul 4;278(27):24294-301. Epub 2003 Apr 21.[pubmed]
  102. Korekane H, Taguchi T, Sakamoto Y, Honke K, Dohmae N, Salminen H, Toivonen S, Helin J, Takio K, Renkonen O, Taniguchi N. "Purification and cDNA cloning of UDP-GlcNAc:GlcNAcbeta1-3Galbeta1-4Glc(NAc)-R [GlcNAc to Gal]beta1,6N-acetylglucosaminyltransferase from rat small intestine: a major carrier of dIGnT activity in rat small intestine." Glycobiology. 2003 May;13(5):387-400. Epub 2003 Jan 22.[pubmed]
  103. Seko A, Dohmae N, Takio K, Yamashita K. "Beta 1,4-galactosyltransferase (beta 4GalT)-IV is specific for GlcNAc 6-O-sulfate. Beta 4GalT-IV acts on keratan sulfate-related glycans and a precursor glycan of 6-sulfosialyl-Lewis X." J Biol Chem. 2003 Mar 14;278(11):9150-8. Epub 2003 Jan 2.[pubmed]
  104. Ishida M, Dohmae N, Shiro Y, Isogai Y. "Synthesis of biotinylated heme and its application to panning heme-binding proteins." Anal Biochem. 2003 Oct 1;321(1):138-41.[pubmed]
  105. Woo SH, Kimura M, Higa-Nishiyama A, Dohmae N, Hamamoto H, Jong SK, Yamaguchi I. "Proteome analysis of wheat lemma." Biosci Biotechnol Biochem. 2003 Nov;67(11):2486-91.[pubmed]
  106. Tsujimura M, Odaka M, Nakayama H, Dohmae N, Koshino H, Asami T, Hoshino M, Takio K, Yoshida S, Maeda M, Endo I. "A novel inhibitor for Fe-type nitrile hydratase: 2-cyano-2-propyl hydroperoxide." J Am Chem Soc. 2003 Sep 24;125(38):11532-8.[pubmed]
  107. Tanioka T, Hattori A, Masuda S, Nomura Y, Nakayama H, Mizutani S, Tsujimoto M. "Human leukocyte-derived arginine aminopeptidase. The third member of the oxytocinase subfamily of aminopeptidases." J Biol Chem. 2003 Aug 22;278(34):32275-83. Epub 2003 Jun 10.[pubmed]
  108. Rajesh S, Nietlispach D, Nakayama H, Takio K, Laue ED, Shibata T, Ito Y. "A novel method for the biosynthesis of deuterated proteins with selective protonation at the aromatic rings of Phe, Tyr and Trp." J Biomol NMR. 2003 Sep;27(1):81-6.[pubmed]
  109. Kitazume S, Tachida Y, Oka R, Kotani N, Ogawa K, Suzuki M, Dohmae N, Takio K, Saido TC, Hashimoto Y. "Characterization of alpha 2,6-sialyltransferase cleavage by Alzheimer's beta -secretase (BACE1)." J Biol Chem. 2003 Apr 25;278(17):14865-71. Epub 2002 Dec 7.[pubmed]
  110. Park YS, Koh YH, Takahashi M, Miyamoto Y, Suzuki K, Dohmae N, Takio K, Honke K, Taniguchi N. "Identification of the binding site of methylglyoxal on glutathione peroxidase: methylglyoxal inhibits glutathione peroxidase activity via binding to glutathione binding sites Arg 184 and 185." Free Radic Res. 2003 Feb;37(2):205-11.[pubmed]

    111. 2002

  111. Yoshikawa N, Dhomae N, Takio K, Abe H. "Purification, properties, and partial amino acid sequences of alanine racemase from the muscle of the black tiger prawn Penaeus monodon." Comp Biochem Physiol B Biochem Mol Biol. 2002 Nov;133(3):445-53.[pubmed]
  112. Nureki O, Shirouzu M, Hashimoto K, Ishitani R, Terada T, Tamakoshi M, Oshima T, Chijimatsu M, Takio K, Vassylyev DG, Shibata T, Inoue Y, Kuramitsu S, Yokoyama S. "An enzyme with a deep trefoil knot for the active-site architecture." Acta Crystallogr D Biol Crystallogr. 2002 Jul;58(Pt 7):1129-37. Epub 2002 Jun 20.[pubmed]
  113. Ueda K, Usui T, Nakayama H, Ueki M, Takio K, Ubukata M, Osada H. "4-isoavenaciolide covalently binds and inhibits VHR, a dual-specificity phosphatase." FEBS Lett. 2002 Aug 14;525(1-3):48-52.[pubmed]
  114. Poltronieri P, Cappello MS, Dohmae N, Conti A, Fortunato D, Pastorello EA, Ortolani C, Zacheo G. "Identification and characterisation of the IgE-binding proteins 2S albumin and conglutin gamma in almond (Prunus dulcis) seeds." Int Arch Allergy Immunol. 2002 Jun;128(2):97-104.[pubmed]
  115. Saito T, Dohmae N, Tsujimoto M, Takio K. "PCR cloning and heterologous expression of cDNA encoding a peptidyl-Lys metalloendopeptidase precursor of Grifola frondosa." J Gen Appl Microbiol. 2002 Oct;48(5):287-92.[pubmed]
  116. Mitsui K, Nakayama H, Akagi T, Nekooki M, Ohtawa K, Takio K, Hashikawa T, Nukina N. "Purification of polyglutamine aggregates and identification of elongation factor-1alpha and heat shock protein 84 as aggregate-interacting proteins." J Neurosci. 2002 Nov 1;22(21):9267-77.[pubmed]
  117. Manya H, Inomata M, Fujimori T, Dohmae N, Sato Y, Takio K, Nabeshima Y, Endo T. "Klotho protein deficiency leads to overactivation of mu-calpain." J Biol Chem. 2002 Sep 20;277(38):35503-8. Epub 2002 Jul 15.[pubmed]
  118. Umezu-Goto M, Kishi Y, Taira A, Hama K, Dohmae N, Takio K, Yamori T, Mills GB, Inoue K, Aoki J, Arai H. "Autotaxin has lysophospholipase D activity leading to tumor cell growth and motility by lysophosphatidic acid production." J Cell Biol. 2002 Jul 22;158(2):227-33. Epub 2002 Jul 15.[pubmed]
  119. Sugawara K, Dohmae N, Kasai K, Saido-Sakanaka H, Okamoto S, Takio K, Ochi K. "Isolation and identification of novel ADP-ribosylated proteins from Streptomyces coelicolor A3(2)." Biosci Biotechnol Biochem. 2002 Oct;66(10):2292-6.[pubmed]
  120. Kubota K, Sakikawa C, Katsumata M, Nakamura T, Wakabayashi K. "PDGF BB purified from osteoclasts acts as osteoblastogenesis inhibitory factor (OBIF)." J Biomol Tech. 2002 Jun;13(2):62-71.[pubmed]
  121. Uchida A, Sugasawa K, Masutani C, Dohmae N, Araki M, Yokoi M, Ohkuma Y, Hanaoka F. "The carboxy-terminal domain of the XPC protein plays a crucial role in nucleotide excision repair through interactions with transcription factor IIH." DNA Repair (Amst). 2002 Jun 21;1(6):449-61.[pubmed]
  122. Sakamoto K, Hayashi A, Sakamoto A, Kiga D, Nakayama H, Soma A, Kobayashi T, Kitabatake M, Takio K, Saito K, Shirouzu M, Hirao I, Yokoyama S. "Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells." Nucleic Acids Res. 2002 Nov 1;30(21):4692-9.[pubmed]
  123. Kiga D, Sakamoto K, Kodama K, Kigawa T, Matsuda T, Yabuki T, Shirouzu M, Harada Y, Nakayama H, Takio K, Hasegawa Y, Endo Y, Hirao I, Yokoyama S. "An engineered Escherichia coli tyrosyl-tRNA synthetase for site-specific incorporation of an unnatural amino acid into proteins in eukaryotic translation and its application in a wheat germ cell-free system." Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9715-20. Epub 2002 Jul 3.[pubmed]
  124. Hashimoto T, Wakabayashi T, Watanabe A, Kowa H, Hosoda R, Nakamura A, Kanazawa I, Arai T, Takio K, Mann DM, Iwatsubo T. "CLAC: a novel Alzheimer amyloid plaque component derived from a transmembrane precursor, CLAC-P/collagen type XXV." EMBO J. 2002 Apr 2;21(7):1524-34.[pubmed]
  125. Fujiwara H, Hasegawa M, Dohmae N, Kawashima A, Masliah E, Goldberg MS, Shen J, Takio K, Iwatsubo T. "alpha-Synuclein is phosphorylated in synucleinopathy lesions." Nat Cell Biol. 2002 Feb;4(2):160-4.[pubmed]
  126. Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, Okuni T, Nakayama H, Takio K, Yabuki T, Kigawa T, Kodama K, Yokogawa T, Nishikawa K, Yokoyama S. "An unnatural base pair for incorporating amino acid analogs into proteins." Nat Biotechnol. 2002 Feb;20(2):177-82.[pubmed]
  127. Kitazume-Kawaguchi Shinobu, Tachida Yuriko, Oka Ritsuko, Kotani Norihiro, Ogawa Kazuko, Suzuki Minoru, Dohmae Naoshi, Takio Koji, Saido Takaomi, Hashimoto Yasuhiro, "Characterization of ST6Gal I cleavage by Alzheimer's BACE1" Glycobiology 2002 12:689
  128. Fukumoto Ryo-hei, Dohmae Naoshi, Takio Koji, Satoh Shinobu, Fujii Tadashi, Sekimoto Hiroyuki, "Purification and characterization of a pheromone that induces sexual cell division in the unicellular green alga {\it Closterium ehrenbergii}" Plant Physiology and Biochemistry 2002 40:183-188 [link]
  129. Akashi Satoko, Takio Koji, "Melittin-diacylphosphatidylcholine interaction examined by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry" Journal of the Mass Spectrometry Society of Japan 2002 50:67-71 [link]

    130. 2001

  130. Natsume T, Nakayama H, Isobe T. "BIA-MS-MS: biomolecular interaction analysis for functional proteomics." Trends Biotechnol. 2001 Oct;19(10 Suppl):S28-33.[pubmed]
  131. Minagawa J, Han KC, Dohmae N, Takio K, Inoue Y. "Molecular characterization and gene expression of lhcb5 gene encoding CP26 in the light-harvesting complex II of Chlamydomonas reinhardtii." Plant Mol Biol. 2001 Jun;46(3):277-87.[pubmed]
  132. Akashi S, Takio K. "Structure of melittin bound to phospholipid micelles studied using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry." J Am Soc Mass Spectrom. 2001 Dec;12(12):1247-53.[pubmed]
  133. Takeda M, Dohmae N, Takio K, Arai K, Watanabe S. "Cell cycle-dependent interaction of Mad2 with conserved Box1/2 region of human granulocyte-macrophage colony-stimulating factor receptor common betac." J Biol Chem. 2001 Nov 9;276(45):41803-9. Epub 2001 Sep 10.[pubmed]
  134. Suzuki Y, Imai Y, Nakayama H, Takahashi K, Takio K, Takahashi R. "A serine protease, HtrA2, is released from the mitochondria and interacts with XIAP, inducing cell death." Mol Cell. 2001 Sep;8(3):613-21.[pubmed]
  135. Gu Y, Misonou H, Sato T, Dohmae N, Takio K, Ihara Y. "Distinct intramembrane cleavage of the beta-amyloid precursor protein family resembling gamma-secretase-like cleavage of Notch." J Biol Chem. 2001 Sep 21;276(38):35235-8. Epub 2001 Aug 1.[pubmed]
  136. Raj VS, Tomitori H, Yoshida M, Apirakaramwong A, Kashiwagi K, Takio K, Ishihama A, Igarashi K. "Properties of a revertant of Escherichia coli viable in the presence of spermidine accumulation: increase in L-glycerol 3-phosphate." J Bacteriol. 2001 Aug;183(15):4493-8.[pubmed]
  137. Ishimura R, Yoshida K, Kimura H, Dohmae N, Takio K, Ogawa T, Tanaka S, Shiota K. "Stage-specific modification of G protein beta subunits in rat placenta." Mol Cell Endocrinol. 2001 Mar 28;174(1-2):77-89.[pubmed]
  138. Kato K, Kishi T, Kamachi T, Akisada M, Oka T, Midorikawa R, Takio K, Dohmae N, Bird PI, Sun J, Scott F, Miyake Y, Yamamoto K, Machida A, Tanaka T, Matsumoto K, Shibata M, Shiosaka S. "Serine proteinase inhibitor 3 and murinoglobulin I are potent inhibitors of neuropsin in adult mouse brain." J Biol Chem. 2001 May 4;276(18):14562-71. Epub 2001 Feb 5.[pubmed]
  139. Nakayama Hiroshi, "Protein functional analysis using liquid chromatography-tandem mass spectrometry in post-genomic era" Chromatography 2001 22:201-207[PDF]
  140. Akasi Satoko, Nakayama Hiroshi, Dohmae Naoshi, Takio Koji, "Utility of mass spectrometry in protein science" RIKEN Review 2001 41:38-40 [PDF]