業績

2017

Okuda M, Nakazawa Y, Guo C, Ogi T, Nishimura Y. Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways. Nucleic Acids Res. 2017 Oct 24. doi: 10.1093/nar/gkx970. [Epub ahead of print]

Ueda H, Kurita J, Neyama H, Hirao Y, Kouji H, Mishina T, Kasai M, Nakano H, Yoshimori A, Nishimura Y. A mimetic of the mSin3-binding helix of NRSF/REST ameliorates abnormal pain behavior in chronic pain models. Bioorg Med Chem Lett. Available online 7 September 2017. doi.org/10.1016/j.bmcl.2017.09.006

Shirai A, Kawaguchi T, Shimojo H, Muramatsu D, Ishida-Yonetani M, Nishimura Y, Kimura H, Nakayama JI, Shinkai Y. Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly. eLIFE. 2017 Aug 1;6. pii: e25317. doi: 10.7554/eLife.25317.

Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H. Crystal structure of the overlapping dinucleosome composed of hexasome and octasome. Science. 2017 Apr 14;356(6334):205-208. doi: 10.1126/science.aak9867.

2016

Okuda M, Araki K, Ohtani K, Nishimura Y. The Interaction Mode of the Acidic Region of the Cell Cycle Transcription Factor DP1 with TFIIH. J Mol Biol. 2016 Nov 5. pii: S0022-2836(16)30467-3. doi: 10.1016/j.jmb.2016.11.001.

Okuda M, Higo J, Komatsu T, Konuma T, Sugase K, Nishimura Y. Dynamics of the Extended String-Like Interaction of TFIIE with the p62 Subunit of TFIIH. Biophys J. 2016 Sep 6;111(5):950-62. doi: 10.1016/j.bpj.2016.07.042.

Moriwaki Y, Yamane T, Ohtomo H, Ikeguchi M, Kurita J, Sato M, Nagadoi A, Shimojo H, Nishimura Y. Solution structure of the isolated histone H2A-H2B heterodimer. Scientific Reports 6, 2016 May 16;6:24999. doi: 10.1038/srep24999.

Shimojo H, Kawaguchi A, Oda T, Hashiguchi N, Omori S, Moritsugu K, Kidera A, Hiragami-Hamada K, Nakayama J, Sato M & Nishimura Y. Extended string-like binding of the phosphorylated HP1α N-terminal tail to the lysine 9-methylated histone H3 tail. Scientific Reports 6, 2016 Mar 3;6:22527. doi: 10.1038/srep22527.

Okuda M, Nishimura Y. Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62. Data Brief. 2016 Jan 2;6:571-7. doi: 10.1016/j.dib.2015.12.034. eCollection 2016 Mar.

Ohtomo H, Akashi S, Moriwaki Y, Okuwaki M, Osakabe A, Nagata K, Kurumizaka H, Nishimura Y. C-terminal acidic domain of histone chaperone human NAP1 is an efficient binding assistant for histone H2A-H2B, but not H3-H4. Genes Cells. 2016 Mar;21(3):252-63., doi: 10.1111/gtc.12339. Epub 2016 Feb 4. (2016)

2015

Okuda M, Kinoshita M, Kakumu E, Sugasawa K, Nishimura Y. Structural Insight into the Mechanism of TFIIH Recognition by the Acidic String of the Nucleotide Excision Repair Factor XPC. Structure. doi: 10.1016/j.str.2015.07.009 (2015).

Okuda M. and Nishimura Y. Real-time and simultaneous monitoring of the phosphorylation and enhanced interaction of p53 and XPC acidic domains with the TFIIH p62 subunit. Oncogenesis 4: e150; doi:10.1038/oncsis.2015.13 (2015).

Saikusa K, Shimoyama S, Asano Y, Nagadoi A, Sato M, Kurumizaka H, Nishimura Y, Akashi S. Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure. Protein Sci. 24, 1224-1231. doi: 10.1002/pro.2673 (2015).

Ichikawa Y, Nishimura Y, Kurumizaka H, Shimizu M. Nucleosome organization and chromatin dynamics in telomeres. Biomol. Concepts. 6, 67-75. doi: 10.1515/bmc-2014-0035 (2015).

Saikusa K, Nagadoi A, Hara K, Fuchigami S, Kurumizaka H, Nishimura Y, Akashi S. Mass spectrometric approach for characterizing the disordered tail regions of the histone H2A/H2B dimer. Anal Chem., 87, 2220-7 (2015).

2014

Nishibuchi G, Machida S, Osakabe A, Murakoshi H, Hiragami-Hamada K, Nakagawa R, Fischle W, Nishimura Y, Kurumizaka H, Tagami H, Nakayama J. N-terminal phosphorylation of HP1α increases its nucleosome-binging specificity. Nucleic Acids Res., 42, 12498-12511 (2014).

Okuda M, Nishimura Y. Extended String Binding Mode of the Phosphorylated Transactivation Domain of Tumor Suppressor p53. J. Am. Chem. Soc., 136, 14143-14152(2014).

Ichikawa Y, Morohashi N, Nishimura Y, Kurumizaka H, Shimizu M. Telomeric repeats act as nucleosome-disfavouring sequences in vivo. Nucleic Acids Res., 42, 1541-52(2014).

2013

Azegami N, Saikusa K, Todokoro Y, Kurumizaka H, Nagadoi A, Nishimura Y, Akashi S. Conclusive evidence of the reconstituted hexasome proved by native mass spectrometry. Biochemistry, 52, 5155-5157 (2013).

Saikusa K, Fuchigami S, Takahashi K, Asano Y, Nagadoi A, Tachiwana H, Kurumizaka H, Ikeguchi M, Nishimura Y, Akashi S. Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation. Gas-phase structure of the histone multimers characterized by ion mobility mass spectrometry and molecular dynamics simulation. Anal Chem. (2013).

2012

Ishida M, Shimojo H, Hayashi A, Kawaguchi R, Ohtani Y, Uegaki K, Nishimura Y, Nakayama J. Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing. Mol Cell. 47, 228-241 (2012).

Okuwaki M, Sumi A, Hisaoka M, Saotome-Nakamura A, Akashi S, Nishimura Y, Nagata K. Function of homo- and hetero-oligomers of human nucleoplasmin/nucleophosmin family proteins NPM1, NPM2 and NPM3 during sperm chromatin remodeling. Nucleic Acids Res. 40, 4861-78 (2012).

2011

Higo J, Nishimura Y, Nakamura H. A free-energy landscape for coupled folding and binding of an intrinsically disordered protein in explicit solvent from detailed all-atom computations. J Am Chem Soc. 133, 10448-10458 (2011).

Horikoshi N, Tachiwana H, Saito K, Osakabe A, Sato M, Yamada M, Akashi S, Nishimura Y, Kagawa W, Kurumizaka H. Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene. Acta Crystallogr D Biol Crystallogr. 67, 112-118 (2011).

2010

Yamane T, Okamura H, Nishimura Y, Kidera A, Ikeguchi M. Side-chain conformational changes of transcription factor PhoB upon DNA binding: a population-shift mechanism. J Am Chem Soc. 132,. 12653-12659 (2010).

Shimoyama S, Nagadoi A, Tachiwana H, Yamada M, Sato M, Kurumizaka H, Nishimura Y, Akashi S., Deimination stabilizes histone H2A/H2B dimers as revealed by electrospray ionization mass spectrometry. J Mass Spectrom. 45, 900-908 (2010).

2008

Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., and Nishimura, Y., Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain. J. Mol. Biol. 378, 987-1001 (2008).

Okuda, M., Tanaka, A., Satoh, M., Mizuta, S., Takazawa, M., Ohkuma, Y., and Nishimura, Y., Structural insight into the TFIIE/TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. EMBO J. 27, 1161-1171 (2008).

Shi, X., Takamizawa, A., Nishimura, Y., Hiraoka, K., Akashi, S., Thermal unfolding of proteins probed by laser spray mass spectrometry. Rapid Commun. Mass Spectrom. 22(9), 1430-1436 (2008).

Sperry, J.B. Shi, X., Rempel, D.L., Nishimura, Y., Akashi, S., Gross, M.L.. A Mass Spectrometric Approach to the Study of DNA-Binding Proteins: The Interaction of Human TRF2 with Telomeric DNA. Biochemsitry, 47, 1797-1807 (2008).

Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A. Water-mediated interactions between DNA and PhoB DNA-binding/ transctivation domain: NMR-restrained molecular dynamics in explicit water environment. PROTEINS: Structure, Function, and Bioinformatics, 71, 1970-83 (2008).

Akashi, S., Nagakura, S., Yamamoto, S., Okuda, M., Ohkuma, Y., Nishimura Y. Structural characterization of human general transcription factor TFIIF in solution. Protein Sci. 17, 389-400 (2008).

2007

Okamura,H.,Makino,K.,Nishimura,Y.:NMR dynamics distinguish between hard and soft hydrophobic cores in the DNA-Binding domain of PhoB and demonstrate different roles of the cores in binding to DNA. J. Mol. Biol. 367, 1093-1117 (2007).

Okuda,M.,Horikoshi,M.,Nishimura Y.:Structural Polymorphism of Chromodomains in Chd1. J. Mol. Biol. 365, 1047-1062 (2007).

Xu, Y., Hirao, Y., Nishimura, Y. and Sugiyama, H. ; I-motif and quadruplex-based device that can control a protein release or bind and release small molecule to influence biological processes., Bioorg. Med. Chem. 15(3), 1275-1279 (2007).

2006

Shi,X.,Takamizawa,A.,Nishimura,Y.,Hiraoka,K., and Akashi,S. Stability analysis for double-stranded DNA oligomers and their noncovalent complexes with drugs by laser spray. J. Mass Spectrom. 41.,1086-1095(2006)

Akashi,S.,Suzuki,K.,Arai,A.,Yamada,N.,Suzuki,E.,Hirayama,K.,Nakamura,S.,and Nishimura,Y. Top-down analysis of basic proteins by microchip capillary electrophoresis mass spectrometry. Rapid Commun. Mass Spectrom.,20, 1932-1938,(2006).

Hirayama, A., Shirota, O., Nomura, M., Nagadoi, A., Nishimura, Y. A protein recycling system for nuclear magnetic resonance-based screening of drug candidates. Analytical Biochem., 353, 99-107 (2006).

Shi,X.,Nishimura,Y.,Akashi,S.,Takamizawa,A.,and Hiraoka,K. Evaluation of Binding Affinity of Protein-Mutant DNA Complexes in Solution by Laser Spray Mass Spectrometry. J Am Soc Mass Spectrom., 17,611-620(2006).

2005

Nomura, M., Uda-Tochio, H., Murai, K., Mori, N., and Nishimura, Y. The Neural Repressor NRSF/REST Binds the PAH1 Domain of the Sin3 Corepressor by Using its Distinct Short Hydrophobic Helix J. Mol. Biol., 354, 903-915 (2005).

Itoh, Y., Unzai, S., Sato, M., Nagadoi, A., Okuda, M., Nishimura, Y., and Akashi, S. Investigation of molecular size of Transcription Factor TFIIE in solution PROTEINS: Structure, Function, and Bioinformatics, 61, 633-641 (2005).

Okuda, M., Tanaka, A., Hanaoka, F., Ohkuma, Y., and Nishimura, Y. Structural Insights into the Asymmetric Effects of Zinc-Ligand Cysteine Mutations in the Novel Zinc Ribbon Domain of Human TFIIEα for Transcription J. Biochem. 138, 443 - 449 (2005)

Akashi, S., Osawa, R., and Nishimura, Y. Evaluation of Protein-DNA Binding Affinity by Electrospray Ionization Mass Spectrometry. J. Amer. Soc. Mass Spectrom. 16, 116-125 (2005).

Hanaoka, S., Nagadoi, A., and Nishimura,Y. Comparison between TRF2 and TRF1 on their telomeric DNA-bound structures and DNA-binding activities. Protein Sci. 14, 119-130 (2005).

2004

Okuda, M., Tanaka, A., Arai, Y., Satoh, M., Okamura, H., Nagadoi, A., Hanaoka, F., Ohkuma, Y., and Nishimura, Y. A Novel Zinc Finger Structure in the Large Subunit of Human General Transcription Factor TFIIE. J. Biol. Chem. 279, 51395-51403 (2004).

Takamizawa, A., Itoh, Y., Osawa, R., Iwasaki, N., Nishimura,Y., Akashi, S., and Hiraoka, K. Selective dissociation of non-covalent bonds in biological molecules by laser spray. J. Mass Spectrom. 39, 1053-1058 (2004).

2002

Shindoh,K., Maenaka, K., Akiba,T.,Okamura, H., Nishimura, Y., Makino, K., and Shirakihara,Y. Crystallization and preliminary X-ray diffraction studies on the DNA-binding domain of the transcriptional activator protein PhoB from Escherichia coli. Acta Crystallogr. D. 58, 1862-1864 (2002).

2001

Nishikawa, T., Okamura, H., Nagadoi, A., König, P., Rhodes, D., and Nishimura, Y. Solution Structure of a Telomeric DNA Complex of Human TRF1. Structure 9, 12237-1251 (2001).

Hanaoka, S., Nagadoi, A., Yoshimura, S., Aimoto, S., Li, B., de Lange, T., and Nishimura, Y. NMR Structure of the hRap1 Myb Motif Reveals a Canonical Three-helix Bundle Lacking the Positive Surface Charge Typical of Myb DNA-Binding Domains. J. Mol. Biol. 312, 167-175 (2001).

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