NISHIMURA Yoshifumi

J-GLOBAL         Last updated: Oct 15, 2019 at 14:45
 
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Name
NISHIMURA Yoshifumi
E-mail
nisimurayokohama-cu.ac.jp
Affiliation
Yokohama City University
Degree
Ph.D.(The University of Tokyo), Master of Pharmaceutical Sciences(The University of Tokyo)

Research Areas

 
 

Academic & Professional Experience

 
Apr 2019
 - 
Today
Vice President,Dean, Graduate School of Integrated Sciences for Life, Hiroshima University
 
Apr 2018
 - 
Today
Project Professor, Graduate School of Medical Life Science, Yokohama City University
 
Apr 2015
 - 
Mar 2018
Advisor to the President, Graduate School of Medical Life Science, Yokohama City University
 
Apr 2013
 - 
Mar 2015
Dean, Graduate School of Medical Life Science, Yokohama City University
 
Apr 1989
 - 
Mar 2013
Professor, Graduate School, Yokohama City University
 

Education

 
Apr 1973
 - 
Mar 1976
Doctor Course, Faculty of Pharmaceutical Sciences, The University of Tokyo
 
Jun 1971
 - 
Mar 1973
Master Course, Faculty of Pharmaceutical Sciences, The University of Tokyo
 
Apr 1967
 - 
May 1971
Faculty of Pharmaceutical Sciences, The University of Tokyo
 

Awards & Honors

 
Jun 2012
The Spectroscopy Society of Japan Award, The Spectroscopical Society of Japan
 

Published Papers

 
Sertraline, chlorprothixene, and chlorpromazine characteristically interact with the REST-binding site of the corepressor mSin3, showing medulloblastoma cell growth inhibitory activities.
Kurita JI, Hirao Y, Nakano H, Fukunishi Y, Nishimura Y.
Sci. Rep.   8 13763   2018   [Refereed]
Structural Diversity of Nucleosomes Characterized by Native Mass Spectrometry.
Saikusa K, Osakabe A, Kato D, Fuchigami S, Nagadoi A, Nishimura Y, Kurumizaka H, Akashi S.
Anal. Chem.   90 8217-8226   2018   [Refereed]
Structural Basis of Homology-Directed DNA Repair Mediated by RAD52
Mika Saotome, Kengo Saito, Takeshi Yasuda, Hideaki Ohtomo, Shusei Sugiyama, Yoshifumi Nishimura, Hitoshi Kurumizaka, Wataru Kagawa.
iScience.   3 50-62   2018   [Refereed]
Common TFIIH recruitment mechanism in global genome and transcription-coupled repair subpathways.
Okuda M., Nakazawa, Y., Guo C., Ogi T., and Nishimura Y.
Nucleic Acids Res.   45(22) 13043-13055   2017   [Refereed]
Ueda H., Kurita J., Neyama H., Hirao Y., Kouji H., Mishina T., Kasai M., Nakano H., Yoshimori A., and Nishimura Y.
Bioorganic Med. Chem. Lett.   27(20) 4705-4709   2017   [Refereed]
Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly.
Shirai A, Kawaguchi T, Shimojo H, Muramatsu D, Ishida-Yonetani M, Nishimura Y, Kimura H, Nakayama JI, Shinkai Y.
eLife   6 25317   2017   [Refereed]
Kato D., Osakabe A., Arimura Y., Mizukami Y., Horikoshi N., Saikusa K., Akashi S., Nishimura Y., Park S-Y., Nogami J., Maehara K., Ohkawa Y., Matsumoto A., Kono H., Inoue R., Sugiyama M., and Kurumizaka H.
Science   356(6334) 205-208   2017   [Refereed]
Shimojo H., Kawaguchi A., Oda T., Hashiguchi N., Omori S., Moritsugu K., Kidera A., Hiragami-Hamada K., Nakayama J., Sato M., Nishimura Y.
Sci. Rep.   6 22527   2016   [Refereed]
Moriwaki Y, Yamane T, Ohtomo H, Ikeguchi M, Kurita J, Sato M, Nagadoi A, Shimojo H, Nishimura Y.
Sci. Rep.   6 24999   2016   [Refereed]
Okuda, M., Araki, K., Ohtani, K., and Nishimura, Y.
J. Mol. Biol.   428 4993-5006   2016   [Refereed]
Okuda M., Higo J., Komatsu Y., Konuma T., Sugase K., and Nishimura Y.
Biophysical J.   111(5) 950-962   2016   [Refereed]
Ohtomo H., Akashi S., Moriwaki Y., Okuwaki M., Osakabe A., Nagata, K., Kurumizaka H., Nishimura Y.
Genes Cells   21 252-263   2016   [Refereed]
Okuda M, Kinoshita M, Kakumu E, Sugasawa K, Nishimura Y.
Structure   23 1827-1837   2015   [Refereed]
Saikusa K, Shimoyama S, Asano Y, Nagadoi A, Sato M, Kurumizaka H, Nishimura Y, Akashi S.
Protein Sci.   24 1224-1231   2015   [Refereed]
Saikusa K, Nagadoi A, Hara K, Fuchigami S, Kurumizaka H, Nishimura Y, Akashi S.
Anal Chem.   87 2220-2227   2015   [Refereed]
Okuda, M. and Nishimura, Y.
J. Am. Chem. Soc   136 14143-14152   2014   [Refereed]
Nishibuchi, G., Machida, S., Osakabe, A., Murakoshi, H., Hiragami-Hamada, K., Nakagawa, R., Fischle, W., Nishimura, Y., Kurumizaka, H., Tagami, H., Nakayama,
Nucleic Acids Res.   42 12498-12511   2014   [Refereed]
Ichikawa Y., Morohashi N., Nishimura Y., Kurumizaka H., Shimizu M.
Nucleic Acids Res.   42 1541-1552   2014   [Refereed]
Azegami N, Saikusa K, Todokoro Y, Kurumizaka H, Nagadoi A, Nishimura Y, Akashi S.
Biochemistry   52 5155-5157   2013   [Refereed]
Ishida M, Shimojo H, Hayashi A, Kawaguchi R, Ohtani Y, Uegaki K, Nishimura Y, Nakayama J.
Mol. Cell   47 228-241   2012   [Refereed]
Mitsuru Okuwaki, Ayako Sumi, Miharu Hisaoka, Ai Saotome-Nakamura, Satoko Akashi, Yoshifumi Nishimura, and Kyosuke Nagata.
Nucleic Acids Res   40 4861-4878   2012   [Refereed]
Junichi Higo, Yoshifumi Nishimura, and Haruki Nakamura.
J. Am. Chem. Soc   133 10448-10458   2011   [Refereed]
Horikoshi N., Tachiwana H., Saito K., Osakabe A., Sato M., Yamada M., Akashi S., Nishimura Y., Kagawa W., and Kurumizaka H.
Acta Crystal. D   67 112-118   2011   [Refereed]
Shingo Shimoyama, Aritaka Nagadoi, Hiroaki Tachiwana, Michiyuki Yamada, Mamoru Sato, Hitoshi Kurumizaka, Yoshifumi Nishimura, and Satoko Akashi.
J. Mass. Spectrom.   45 900-908   2010   [Refereed]
Yamane T, Okamura H, Nishimura Y, Kidera A, Ikeguchi M.
J. Am. Chem. Soc.   132 12653-12659   2010   [Refereed]
Shi X, Takamizawa A, Nishimura Y, Hiraoka K, Akashi S
Rapid Commun. Mass Spectrom.   22(9) 1430-1436   2008   [Refereed]
Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., and Nishimura, Y.
J. Mol. Biol.   378 987-1001   2008   [Refereed]
Okuda, M., Tanaka, A., Satoh, M., Mizuta, S., Takazawa, M., Ohkuma, Y., and Nishimura, Y.
EMBO J.   27 1161-1171   2008   [Refereed]
Akashi, S., Nagakura, S., Yamamoto, S., Okuda, M., Ohkuma, Y., Nishimura Y.
Protein Sci.   17 389-400   2008   [Refereed]
Sperry, J.B. Shi, X., Rempel, D.L., Nishimura, Y., Akashi, S., Gross, M.L.
Biochemsitry   47 1797-1807   2008   [Refereed]
Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A
PROTEINS: Structure, Function, and Bioinformatics   71 1970-1983   2008   [Refereed]
Okuda,M.,Horikoshi,M.,Nishimura Y.
J. Mol. Biol.   365 1047-1062   2007   [Refereed]
Xu, Y., Hirao, Y., Nishimura, Y., Sugiyama, H.
Bioorganic & Medicinal Chemistry.   15 1275-1279   2007   [Refereed]
Shi,X.,Takamizawa,A.,Nishimura,Y.,Hiraoka,K., and Akashi,S.
J. Mass Spectrom.   41 1086-1095   2006   [Refereed]
Akashi,S.,Suzuki,K.,Arai,A.,Yamada,N.,Suzuki,E.,Hirayama,K.,Nakamura,S.,and Nishimura,Y.
Rapid Commun. Mass Spectrom.   20 1932-1938   2006   [Refereed]
Hirayama, A., Shirota, O., Nomura, M., Nagadoi, A., Nishimura, Y.
Analytical Biochem.   353 99-107   2006   [Refereed]
Akashi, S., Osawa, R., and Nishimura, Y.
J. Amer. Soc. Mass Spectrom.   16 116-125   2005   [Refereed]
Hanaoka, S., Nagadoi, A., and Nishimura,Y.
Protein Sci.   14 119-130   2005   [Refereed]
Shi,X.,Nishimura,Y.,Akashi,S.,Takamizawa,A.,and Hiraoka,K.
J Am Soc Mass Spectrom.   17 611-620   2005   [Refereed]
Nomura, M., Uda-Tochio, H., Murai, K., Mori, N., and Nishimura, Y.
J. Mol. Biol.   354 903-915   2005   [Refereed]
Itoh, Y., Unzai, S., Sato, M., Nagadoi, A., Okuda, M., Nishimura, Y., and Akashi, S.
PROTEINS: Structure, Function, and Bioinformatics,   61 633-641   2005   [Refereed]
Okuda, M., Tanaka, A., Hanaoka, F., Ohkuma, Y., and Nishimura, Y.
J. Biochem.   138 443-449   2005   [Refereed]
Okuda, M., Tanaka, A., Arai, Y., Satoh, M., Okamura, H., Nagadoi, A., Hanaoka, F., Ohkuma, Y., and Nishimura, Y.
J. Biol. Chem.   279 51395-51403   2004   [Refereed]
Takamizawa, A., Itoh, Y., Osawa, R., Iwasaki, N., Nishimura,Y., Akashi, S., and Hiraoka, K.
J. Mass Spectrom.   39 1053-1058   2004   [Refereed]

Misc

 
Comparison of DNA-binding activities between hTRF2 and hTRF1 with hTRF2 mutants.
NISHIMURA Yoshifumi
Modern Magnetic Resonance   1    2006
NISHIMURA Yoshifumi
Structure 9   12237-1251    2001
NISHIMURA Yoshifumi
Biophysics & Molecular Biology   73    2000
Backbone Dynamics of the c-Myb DNA-binding Domain Complexed with a Specific DNA. (共著)
NISHIMURA Yoshifumi
J. Biochem.   127/,945-953    2000
Solution structure of the DNA-binding domain of human telomeric protein, hTRf1.
NISHIMURA Yoshifumi
Structure   6/,1057-1065    1998
Identification of indispensable residues for specific DNA-binding in the imperfect tandem repeates of c-Myb R2R3.
NISHIMURA Yoshifumi
Protein Engineering   10/,1407-1414    1997
NISHIMURA Yoshifumi
J. Biol. Chem.   272/,7381-7389    1997
NISHIMURA Yoshifumi
Eur. J. Biochemistry   236/,533-538    1996
Amide proton exchange rates in c-Myb DNA-binding domain(共著)
NISHIMURA Yoshifumi
Quat. Magn. Res. in Biol. Med   3/,33-45    1996
Determination of the nuclear magnetic resonance solution structure of a specific DNA complex of the Myb DNA-binding domain. (共著)
NISHIMURA Yoshifumi
J. biomol. NMR   6/,294-305    1995
Structural comparison of the free and DNA-bound forms of the purine repressor DNA-binding domain(共著)
NISHIMURA Yoshifumi
Structure   3/,1217-1224    1995
Comparison of the free and DNA-complexed forms of the DNA-binding domain from c-Myb(共著)
NISHIMURA Yoshifumi
Nature Structural Biology   2/,309-320    1995
Resonance Raman and Fourier Transform Infrared Studies on the Subunit I Histigine Mutants of the Cytochrome bo Complex in Escherichia coli(共著)
NISHIMURA Yoshifumi
J. Biol. Chem.   269/,11912-11920    1994
A Raman Spectroscopic Study on Conformations of DNA Oligomers : a dominant Efect of an AA : TT Sequence over those of AT : AT and TA : TA Sequences on Determining Conformations of DNA Duplexes(共著)
NISHIMURA Yoshifumi
Nucleosides & Nucleotides   13/,1467-1481    1994
Crystallization and X-ray Studies of the DNA-binding Domain of OmpR Protein, a Positive Regulator Involved in Activation of Osmoregulatory Genes in Escherichia coli(共著)
NISHIMURA Yoshifumi
J. Mol. Biol.   235/,780-782    1994
NISHIMURA Yoshifumi
Biochemistry   32/,7759-7764    1993
Activation of the osmoregulated┣DBompC(/)-┫DB gene by the OmpR protein in ┣DBEscherichia(/)-┫DB ┣DBcoli(/)-┫DB A study involving synthetic OmpR-binding sequences. (共著)
NISHIMURA Yoshifumi
J. Biochem.   110    1991
The tryptophan cluster : A hypothetical structure of the DNA-binding domain of the ┣DBmyb(/)-┫DB protooncogen product. (共著)
NISHIMURA Yoshifumi
J. Biological Chemistry   265    1990
NISHIMURA Yoshifumi
Chem. Pharm. Bull.   37/,422-424    1989
Proton Nuclear Magnetic Resonance Study of a Selectively Deuterated Mouse Monoclonal Antibody : Use of Two Dimensional Homonuclear Hartman Hahn Spectroscopy(共著)
NISHIMURA Yoshifumi
J. Biochem.   106/,361-364    1989
Applications of 13C Nuclear Magnetic Resonance Spectroscopy to the Molecular Structural Analyses of the Antibody Molecule(共著)
NISHIMURA Yoshifumi
J. Biochem.   105/,867-869    1989
Quantitative treatment of photochemically effects on the ultraviolet resonance Raman spectroscopic intensities. (共著)
NISHIMURA Yoshifumi
J. American Chemical Soc.   109    1987
Two types of conformers with distinct Fe-C-O configuration in the ferrous CO complex of horseradish peroxidase. (共著)
NISHIMURA Yoshifumi
J. Biological Chemistry   262    1987
A Raman spectroscopic analysis of the sequence-dependent structure of oligo-DNA duplexes : d(CGCG)2, d(GCGC)2, d(GGCC)2 and d(CCGG)2 in aqueous solution. (共著)
NISHIMURA Yoshifumi
Spectrochim. Acta.   42A    1986
Local and overall conformations of DNA double helices with the A-T base pairs. (共著)
NISHIMURA Yoshifumi
Biochim. Biophys. Acta   867    1986
Coordination structures and reactivities of compound II in iron and manganese horseradish peroxidase. (共著)
NISHIMURA Yoshifumi
J. Biological Chemistry   261    1986
NISHIMURA Yoshifumi
Surface Sci.   158/,341-351    1985
NISHIMURA Yoshifumi
Chemical Physics   100/,365-375    1985
The resonance Raman frequencies of the Fe-CO stretching and bending modes in the CO complex of cytochrome P-450cam. (共著)
NISHIMURA Yoshifumi
J. Biological Chemistry   260    1985
NISHIMURA Yoshifumi
Bioplymers   24    1985
Resonence Raman study of cytochrome b562-o complex, a terminal oxidase of ┣DBEscherichia(/)-┫DB ┣DBcoli(/)-┫DB in its ferric-, ferrous-and Co-ligated states. (共著)
NISHIMURA Yoshifumi
J. Biological Chemistry   260    1985
NISHIMURA Yoshifumi
Biopolymers   24    1985
A possible correlation between DNA conformations and the mode of action of restriction enzymes. (共著)
NISHIMURA Yoshifumi
J. Biochemistry   96    1984
Dynamics of DNA in chromatin and DNA binding mode to core protein. (共著)
NISHIMURA Yoshifumi
J. Biochmistry   93    1983
Microenvironment of the H3-H3 contact region of a nucleosome core particleas revealed by life time measurement of a fluorescent probe. (共著)
NISHIMURA Yoshifumi
J. Biochemistry   92    1982
Lifetime of tyrosine fluorescence in nucleosome core particle. (共著)
NISHIMURA Yoshifumi
J. Biochemistry   91    1982
NISHIMURA Yoshifumi
Bulletin Chemical Society of Japan   53    1980
NISHIMURA Yoshifumi
Chemical Physics Letters   59    1979
NISHIMURA Yoshifumi
Bulletin Chemical Socity of Japan   52    1979
Crystallization of arginine-, formylmethionine-, tyrosine-, and glycine-transfer RNAs from ┣DBEscherichia coli(/)-┫DB(共著)
NISHIMURA Yoshifumi
J. Biochem.   84/,369-375    1978
NISHIMURA Yoshifumi
J. Raman Spectroscopy   7    1978
NISHIMURA Yoshifumi
Chemistry Letters   1977    1977
NISHIMURA Yoshifumi
J. Molecular Spectroscopy   68    1977
NISHIMURA Yoshifumi
Nature   260    1976
NISHIMURA Yoshifumi
Bulletin Chemical Society Japan   47    1974

Books etc

 
Three-dimensional structure of the DNA-binding domain of a protooncogene product, Myb. "Molecular Structure and Life : Molecular Recognition of Nucleic Acid"(共著)
Japan Scientific Soc. Press   1992   
Resonance Raman spectroscopy and nomal modes of the nucleic acid bases. (共著) "Biological Application of Raman Spectrometry, vol. 2, Resonance Raman Spectra of Polyenes and Aromatics"
John Wiley and Sons, Inc.   1987   
Active site conformations of horseradish peroxidase as revealed by time resolved resonance Raman spectroscopy. (共著) "Time Resolved Vibrational Spectroscopy"
Gorden and Breach Science Publishers   1987   
Local conformations and polymorphism of DNA duplexes as revealed by their Raman spectra. (共著) "Spectroscopy of Biological Systems"
John Wiely and Sons, Inc.   1986   
Sequence dependent DNA conformations : Raman spectroscopic studies and a mode of action of restriction enzymes. "Advances in Biophysics, vol. 20"
Japan Scientific Socity Press   1985   

Conference Activities & Talks

 
Solution structures of chromatin-related proteins
2ndBilateral Japan-UK Symposium   2005   
Structural biology of chromatin-related proteins
International Symposium on Stable Isotope Aided Biological NMR   2005   
Solution structures of chromatin-related proteins
2005   
Solution structure of the hydrophobic helix of NRSF/REST bound to the PAH1 domain of mSin3B
The44th NMR Meeting of the NMR Society of Japan and The 1st Asia-Pacific NMR Symposium   2005   
Specific Interaction of Human TRF2 with a G-quadruplex Structure
The44th NMR Meeting of the NMR Society of Japan and The 1st Asia-Pacific NMR Symposium   2005   

Research Grants & Projects

 
Structural Analyses of Signal-Recognizing Proteins
Structural Analyses of DNA・Protein Complexes
Structural Analyses of Telomeres