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2024
Sako K, Furukawa A, Nozawa RS, Kurita JI, Nishimura Y, Hirota T. Bipartite binding interface recruiting HP1 to chromosomal passenger complex at inner centromeres. J Cell Biol. 2024 Sep 2;223(9):e202312021. doi: 10.1083/jcb.202312021. Epub 2024 May 23.
Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep. 2024 Feb 27;43(2):113697. doi: 10.1016/j.celrep.2024.113697. Epub 2024 Jan 30.
2023
Ohtomo H, Yamane T, Oda T, Kodera N, Kurita JI, Tsunaka Y, Amyot R, Ikeguchi M, Nishimura Y. Dynamic Solution Structures of Whole Human NAP1 Dimer Bound to One and Two Histone H2A-H2B Heterodimers Obtained by Integrative Methods. J Mol Biol. 2023 Aug 1;435(15):168189. doi: 10.1016/j.jmb.2023.168189. Epub 2023 Jun 26.
Okuda M, Nishimura Y. Structural polymorphism of the PH domain in TFIIH.Biosci Rep.2023 Jul 26;43(7):BSR20230846. doi: 10.1042/BSR20230846.
Konuma T, Kurita JI, Ikegami T. CPMG pulse sequence for relaxation dispersion that cancels artifacts independently of spin states. J Magn Reson. 2023 Jul;352:107489. doi: 10.1016/j.jmr.2023.107489. Epub 2023 May 21.
Ohtomo H, Ito S, McKenzie NJ, Uckelmann M, Wakamori M, Ehara H, Furukawa A, Tsunaka Y, Shibata M, Sekine SI, Umehara T, Davidovich C, Koseki H, Nishimura Y. H2A Ubiquitination Alters H3-tail Dynamics on Linker-DNA to Enhance H3K27 Methylation.J Mol Biol.2023 Feb 28;435(4):167936. doi: 10.1016/j.jmb.2022.167936. Epub 2023 Jan 4.
2022
Furukawa A, Wakamori M, Arimura Y, Ohtomo H, Tsunaka Y, Kurumizaka H, Umehara T, Nishimura Y. Erratum: Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome. iScience. 2022 Oct 25;25(11):105408. doi: 10.1016/j.isci.2022.105408. eCollection 2022 Nov 18.
Tsunaka Y, Ohtomo H, Nishimura Y. FACT modulates the conformations of histone H2A and H2B N-terminal tails within nucleosomes. Commun Biol. 2022 Aug 13;5(1):814. doi: 10.1038/s42003-022-03785-z.
Arisawa T, Kimura K, Miyazaki T, Takada Y, Nakajima W, Ota W, Ichijo S, Sano A, Hirao Y, Kurita JI, Nishimura Y, Takahashi T. Synthesis of [ 18 F] fluorine-labeled K-2 derivatives as radiotracers for AMPA receptors. Nucl Med Biol. 2022 Jul-Aug;110-111:47-58. doi: 10.1016/j.nucmedbio.2022.04.009. Epub 2022 Apr 30.
Furukawa A, Wakamori M, Arimura Y, Ohtomo H, Tsunaka Y, Kurumizaka H, Umehara T, Nishimura Y. Characteristic H3 N-tail dynamics in the nucleosome core particle, nucleosome, and chromatosome. iScience. 2022 Feb 17;25(3):103937. doi: 10.1016/j.isci.2022.103937. eCollection 2022 Mar 18.
Okuda M, Suwa T, Suzuki H, Yamaguchi Y, Nishimura Y. Three human RNA polymerases interact with TFIIH via a common RPB6 subunit. Nucleic Acids Res. 2022 Jan 11;50(1):1-16. doi: 10.1093/nar/gkab612.
2021
Zhang R, Isozumi N, Mori M, Okuta R, Singkaravanit-Ogawa S, Imamura T, Kurita JI, Gan P, Shirasu K, Ohki S, Takano Y.Fungal effector SIB1 of Colletotrichum orbiculare has unique structural features and can suppress plant immunity in Nicotiana benthamiana.J Biol Chem. 2021 Dec;297(6):101370. doi: 10.1016/j.jbc.2021.101370. Epub 2021 Oct 29.
Ohtomo H, Kurita JI, Sakuraba S, Li Z, Arimura Y, Wakamori M, Tsunaka Y, Umehara T, Kurumizaka H, Kono H, Nishimura Y. The N-terminal Tails of Histones H2A and H2B Adopt Two Distinct Conformations in the Nucleosome with Contact and Reduced Contact to DNA. J Mol Biol. 2021 Jun 18;433(15):167110. doi: 10.1016/j.jmb.2021.167110. Epub 2021 Jun 18.
Okuda M, Ekimoto T, Kurita JI, Ikeguchi M, Nishimura Y. Structural and dynamical insights into the PH domain of p62 in human TFIIH. Nucleic Acids Res. 2021 Mar 18;49(5):2916-2930. doi: 10.1093/nar/gkaa1045.
Hayami T, Kamiya N, Kasahara K, Kawabata T, Kurita JI, Fukunishi Y, Nishimura Y, Nakamura H, Higo J. Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities. Sci Rep. 2021 Mar 17;11(1):6178. doi: 10.1038/s41598-021-85612-9.
Matsumura K, Shimomura T, Kubo Y, Oka T, Kobayashi N, Imai S, Yanase N, Akimoto M, Fukuda M, Yokogawa M, Ikeda K, Kurita JI, Nishimura Y, Shimada I, Osawa M. Mechanism of hERG inhibition by gating-modifier toxin, APETx1, deduced by functional characterization. BMC Mol Cell Biol. 2021 Jan 7;22(1):3. doi: 10.1186/s12860-020-00337-3.
2020
Furukawa A, Walinda E, Arita K, Sugase K. Structural dynamics of double-stranded DNA with epigenome modification. Nucleic Acids Res. 2020 Dec 18:gkaa1210. doi: https://doi.org/10.1093/nar/gkaa1210
Tsunaka Y, Ohtomo H, Morikawa K, Nishimura Y. Partial replacement of nucleosomal DNA with human FACT induces dynamic exposure and acetylation of histone H3 N-terminal tails. iScience. 2020 Oct 6;23(10):101641. doi: 10.1016/j.isci.2020.101641. eCollection 2020 Oct 23.
Furukawa A, Wakamori M, Arimura Y, Ohtomo H, Tsunaka Y, Kurumizaka H, Umehara T, Nishimura Y. Acetylated histone H4 tail enhances histone H3 tail acetylation by altering their mutual dynamics in the nucleosome. Biosci Rep. PNAS August 3, 2020. https://doi.org/10.1073/pnas.2010506117
Okuda M, Nishimura Y. The Eaf3 chromodomain acts as a pH sensor for gene expression by altering its binding affinity for histone methylated-lysine residues. Biosci Rep. 2020 Feb 28;40(2):BSR20191958. doi: 10.1042/BSR20191958.
2019
Mayanagi K, Saikusa K, Miyazaki N, Akashi S, Iwasaki K, Nishimura Y, Morikawa K, Tsunaka Y. Structural visualization of key steps in nucleosome reorganization by human FACT. Sci Rep. 2019 Jul 15;9(1):10183. doi: 10.1038/s41598-019-46617-7.
2018
Saotome M, Saito K, Yasuda T, Ohtomo H, Sugiyama S, Nishimura Y, Kurumizaka H, Kagawa W. Structural Basis of Homology-Directed DNA Repair Mediated by RAD52. iScience. 2018 May 25;3:50-62. doi: 10.1016/j.isci.2018.04.005. Epub 2018 Apr 12.
Kurita JI, Hirao Y, Nakano H, Fukunishi Y, Nishimura Y. Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities. Sci Rep. 2018 Sep 13;8(1):13763. doi: 10.1038/s41598-018-31852-1.
Saikusa K, Osakabe A, Kato D, Fuchigami S, Nagadoi A, Nishimura Y, Kurumizaka H, Akashi S. Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry. Anal Chem. 2018 Jul 3;90(13):8217-8226. doi: 10.1021/acs.analchem.8b01649. Epub 2018 Jun 12.
Konuma T, Nagadoi A, Kurita J, Ikegami T. Analysis of artifacts caused by pulse imperfections in CPMG pulse trains in NMR relaxation dispersion experiments. Magnetochemistry. 2018, 4(3), 33.
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 Dec 15; 45(22):13043-13055. doi: 10.1093/nar/gkx970.
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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