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自治医科大学 医学部 生理学講座 生物物理学部門

研究成果PUBLICATIONS

発表論文

  • 2017
    1. Direct observation of conformational population shifts in crystalline human hemoglobin
      Shibayama N, Ohki M, Tame JRH, Park SY
      The Journal of Biological Chemistry 292, 18258-18269 2017年9月
      http://www.jbc.org/content/292/44/18258.short
    2. Size and Shape Controlled Crystallization of Hemoglobin for Advanced Crystallography.
      Sato-Tomita S, Shibayama N
      Crystals 7(9), 282 2017年9月
      http://www.mdpi.com/2073-4352/7/9/282
    3. Ligation-Dependent Picosecond Dynamics in Human Hemoglobin As Revealed by Quasielastic Neutron Scattering.
      Fujiwara S, Chatake T, Matsuo T, Kono F, Tominaga T, Shibata K, Sato-Tomita A, Shibayama N
      The journal of physical chemistry B 121(34) 8069-8077 2017年8月
      http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b05182
    4. Molecular mechanism of photoactivation of a light-regulated adenylate cyclase.
      Ohki M, Sato-Tomita A, Matsunaga S, Iseki M, Tame JRH, Shibayama N, Park SY
      Proceedings of the National Academy of Sciences of the United States of America 114(32) 8562-8567 2017年8月
      http://www.pnas.org/content/114/32/8562
    5. Protein crystallography beamline BL2S1 at the Aichi synchrotron.
      Watanabe N, Nagae T, Yamada Y, Tomita A, Matsugaki N, Tabuchi M
      J Synchrotron Radiat. 24(Pt 1) 338-43 2017年1月
      https://doi.org/10.1107/S1600577516018579
  • 2016
    1. Development of an X-ray fluorescence holographic measurement system for protein crystals.
      Sato-Tomita A, Shibayama N, Happo N, Kimura K, Okabe T, Matsushita T, Park SY, Sasaki YC, Hayashi K
      The Review of scientific instruments 87(6) 063707 2016年6月
      http://dx.doi.org/10.1063/1.4953453
    2. Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium.
      Ohki M, Sugiyama K, Kawai F, Tanaka H, Nihei Y, Unzai S, Takebe M, Matsunaga S, Adachi S, Shibayama N, Zhou ZW, Koyama R, Ikegaya Y, Takahashi T, Tame JRH, Iseki M, Park SY
      Proceedings of the National Academy of Sciences of the United States of America 113(24) 6659-6664 2016年6月
      http://www.pnas.org/content/113/24/6659
  • 2015
    1. Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair.
      Shinohara T, Ikawa S, Iwasaki W, Hiraki T, Hikima T, Mikawa T, Arai N, Kamiya N, Shibata T
      Nucleic acids research 43(2) 973-986 2015年01月
      http://dx.doi.org/10.1093/nar/gku1364
    2. Cooling dynamics of self-assembled monolayer coating for integrated gold nanocrystals on a glass substrate.
      Ichiyanagi K, Sekiguchi H, Sato T, Nozawa S, Tomita A, Hoshino M, Adachi S, Sasaki YC
      Journal of synchrotron radiation 22(Pt 1) 29-33 2015年01月
      http://dx.doi.org/10.1107/S1600577514019730
  • 2014
    1. ポンプ−プローブ法を用いた生体分子の構造ダイナミクス測定
      富田 文菜, 野澤 俊介, 足立 伸一, 佐藤 篤志, 柴山 修哉
      日本結晶学会誌 56(4) 253-258 2014年08月
      http://dx.doi.org/10.5940/jcrsj.56.253
    2. Delineation of Solution Burst-Phase Protein Folding Events by Encapsulating the Proteins in Silica Gels.
      Okabe T, Tsukamoto S, Fujiwara K, Shibayama N, Ikeguchi M
      Biochemistry. 53(23) 3858-66 2014年6月
      http://pubs.acs.org/doi/abs/10.1021/bi5003647
    3. Capturing the hemoglobin allosteric transition in a single crystal form.
      Shibayama N, Sugiyama K, Tame JR, Park SY
      Journal of the American Chemical Society 136 5097-5105 2014年04月
      http://dx.doi.org/10.1021/ja500380e
  • 2013
    1. Intersubunit communication via changes in hemoglobin quaternary structures revealed by time-resolved resonance Raman spectroscopy: direct observation of the Perutz mechanism.
      Yamada K, Ishikawa H, Mizuno M, Shibayama N, Mizutani Y
      The journal of physical chemistry. B 117 12461-12468 2013年10月
      http://dx.doi.org/10.1021/jp407735t
    2. Pressure-induced endocytic degradation of the Saccharomyces cerevisiae low-affinity tryptophan permease Tat1 is mediated by Rsp5 ubiquitin ligase and functionally redundant PPxY motif proteins.
      Suzuki A, Mochizuki T, Uemura S, Hiraki T, Abe F
      Eukaryotic cell 12(7) 990-997 2013年07月
      http://dx.doi.org/10.1128/EC.00049-13
    3. Brevundimonas abyssalis sp. nov., a dimorphic prosthecate bacterium isolated from deep-subsea floor sediment.
      Tsubouchi T, Shimane Y, Usui K, Shimamura S, Mori K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y
      International journal of systematic and evolutionary microbiology 63(Pt 6) 1987-1994 2013年06月
      http://dx.doi.org/10.1099/ijs.0.043364-0
    4. Polycladomyces abyssicola gen. nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment.
      Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T, Tame A, Uematsu K, Maruyama T, Hatada Y
      International journal of systematic and evolutionary microbiology 63(Pt 6) 1972-1981 2013年06月
      http://dx.doi.org/10.1099/ijs.0.043596-0
    5. Homopiperazine derivatives as a novel class of proteasome inhibitors with a unique mode of proteasome binding.
      Kikuchi J, Shibayama N, Yamada S, Wada T, Nobuyoshi M, Izumi T, Akutsu M, Kano Y, Sugiyama K, Ohki M, Park SY, Furukawa Y
      PloS one 8 e60649 2013年
      http://dx.doi.org/10.1371/journal.pone.0060649
  • 2012
    1. Symmetry distortion in the human hemoglobin tetramer induced by asymmetric ligation.
      Shibayama N
      FEBS letters 586 74-78 2012年01月
      http://dx.doi.org/10.1016/j.febslet.2011.11.027
  • 2011
    1. Structures and oxygen affinities of crystalline human hemoglobin C (β6 Glu->Lys) in the R and R2 quaternary structures.
      Shibayama N, Sugiyama K, Park SY
      The Journal of biological chemistry 286 33661-33668 2011年09月
      http://dx.doi.org/10.1074/jbc.M111.266056
    2. MWC2状態モデルはヘモグロビンのアロステリーといかに調和しうるか
      柴山修哉
      人工血液 18(3) 102-109 2011年01月

  • 2010-2001
    1. Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography.
      Kovalevsky A, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher SZ, Langan P, Morimoto Y
      Acta crystallographica. Section D, Biological crystallography 66 1144-1152 2010年11月
      http://dx.doi.org/10.1107/S0907444910025448
    2. Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect.
      Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher Z, Langan P, Morimoto Y
      Journal of molecular biology 398 276-291 2010年04月
      http://dx.doi.org/10.1016/j.jmb.2010.03.016
    3. Physicochemical properties of diheme cytochrome c4 of unknown function from Vibrio parahaemolyticus strain RIMD2210633.
      Akazaki H, Futami Y, Shibayama N, Shirasaki I, Nakade H, Chida H, Hakamata W, Park SY, Nishio T, Oku T
      Bioscience, biotechnology, and biochemistry 72 2791-2794 2008年10月
    4. The structural basis for an essential subunit interaction in influenza virus RNA polymerase.
      Obayashi E, Yoshida H, Kawai F, Shibayama N, Kawaguchi A, Nagata K, Tame JR, Park SY
      Nature 454 1127-1131 2008年08月
      http://dx.doi.org/10.1038/nature07225
    5. Circular dichroism study on the early folding events of beta-lactoglobulin entrapped in wet silica gels.
      Shibayama N
      FEBS letters 582 2668-2672 2008年07月
      http://dx.doi.org/10.1016/j.febslet.2008.06.047
    6. Slow motion analysis of protein folding intermediates within wet silica gels.
      Shibayama N
      Biochemistry 47 5784-5794 2008年05月
      http://dx.doi.org/10.1021/bi8003582
    7. Preliminary time-of-flight neutron diffraction study of human deoxyhemoglobin.
      Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher SZ, Langan P, Morimoto Y
      Acta Crystallogr F. 64 270-273 2008年4月
      https://doi.org/10.1107/S1744309108005137
    8. Crystal structures of the clock protein EA4 from the silkworm Bombyx mori.
      Hiraki T, Shibayama N, Akashi S, Park SY
      Journal of molecular biology 377(3) 630-635 2008年03月
      http://dx.doi.org/10.1016/j.jmb.2008.01.020
    9. Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography.
      Chatake T, Shibayama N, Park SY, Kurihara K, Tamada T, Tanaka I, Niimura N, Kuroki R, Morimoto Y
      Journal of the American Chemical Society 129 14840-14841 2007年12月
      http://dx.doi.org/10.1021/ja0749441
    10. Crystallization and preliminary crystallographic studies of the metalloglycoprotein esterase A4 using a baculovirus expression system.
      Hiraki T, Shibayama N, Yoon YH, Yun KM, Hamamoto T, Tame JR, Park SY
      Acta crystallographica. Section F, Structural biology and crystallization communications 63 734-736 2007年09月
      http://dx.doi.org/10.1107/S1744309107033854
    11. 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms.
      Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR
      Journal of molecular biology 360 690-701 2006年07月
      http://dx.doi.org/10.1016/j.jmb.2006.05.036
    12. Crystal structures of unliganded and half-liganded human hemoglobin derivatives cross-linked between Lys 82beta1 and Lys 82beta2.
      Park SY, Shibayama N, Hiraki T, Tame JR
      Biochemistry 43 8711-8717 2004年07月
      http://dx.doi.org/10.1021/bi049932w
    13. 光解離に伴うヘモグロビンの動きを観る
      柴山修哉
      生物物理 44(3) 108-112 2004年
      http://dx.doi.org/10.2142/biophys.44.108
    14. Highly nonexponential kinetics in the early-phase refolding of proteins at low temperatures.
      Saigo S, Shibayama N
      Biochemistry 42 9669-9676 2003年08月
      http://dx.doi.org/10.1021/bi034484y
    15. Direct observation of photolysis-induced tertiary structural changes in hemoglobin.
      Adachi S, Park SY, Tame JR, Shiro Y, Shibayama N
      Proceedings of the National Academy of Sciences of the United States of America 100 7039-7044 2003年06月
      http://dx.doi.org/10.1073/pnas.1230629100
    16. Oxygen equilibrium properties of myoglobin locked in the liganded and unliganded conformations.
      Shibayama N, Saigo S
      Journal of the American Chemical Society 125 3780-3783 2003年04月
      http://dx.doi.org/10.1074/jbc.M205461200
    17. Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-A resolution. A novel allosteric binding site in R-state hemoglobin.
      Shibayama N, Miura S, Tame JR, Yonetani T, Park SY
      The Journal of biological chemistry 277 38791-38796 2002年10月
      http://dx.doi.org/10.1074/jbc.M205461200
    18. The contribution of the asymmetric alpha 1beta 1 half-oxygenated intermediate to human hemoglobin cooperativity.
      Yun KM, Morimoto H, Shibayama N
      The Journal of biological chemistry 277 1878-1883 2002年01月
      http://dx.doi.org/10.1074/jbc.M108494200
    19. Differences in changes of the α1-β2 subunit contacts between ligand binding to the α and β subunits of hemoglobin A: UV resonance Raman analysis using Ni-Fe hybrid hemoglobin
      Nagatomo, S., Nagai, M., Shibayama, N., and Kitagawa, T.
      Biochemistry 41 10010-10020 2002年
    20. Direct observation of two distinct affinity conformations in the T state human deoxyhemoglobin
      Shibayama, N., and Saigo, S.
      FEBS Letters 492 50-53 2001年

  • 2000-1991
    1. ゾル・ゲル法でタンパク質分子のコンホメーションを固定する
      柴山修哉
      生物物理 40(5) 346-349 2000年
      http://dx.doi.org/10.2142/biophys.40.346
    2. Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme
      Miyazaki, G. et al.
      Journal of Molecular Biology 292 1121-1136 1999年
    3. Functional analysis of hemoglobin molecules locked in doubly liganded conformations.
      Shibayama, N.
      Journal of Molecular Biology 285 1383-1388 1999年
    4. Kinetics of the allosteric transition in hemoglobin within silicate sol-gels
      Shibayama, N., and Saigo, S.
      Journal of the American Chemical Society 121 444-445 1999年
    5. Asymmetric cyanomet valency hybrid hemoglobin, (α+CN-β+CN-)(αβ): The Issue of valency exchange
      Shibayama, N., Morimoto, H., and Saigo, S.
      Biochemistry 37 6221-6228 1998年
    6. Rate constants for O2 and CO binding to the alpha and beta subunits within the R and T states of human hemoglobin
      Unzai, S., Eich, R., Shibayama, N., Olson, J. S., and Morimoto, H.
      Journal of Biological Chemistry 273 23150-23159 1998年
    7. 作用反作用の法則は誤解されている
      青野修, 西郷敏, 原田三男, 柴山修哉
      物理教育 45(6) 328-329 1997年12月
    8. Reexamination of the hyper thermodynamic stability of asymmetric cyanomet valency hybrid hemoglobin, (α+CN-β+CN-)(αβ): No preferentially populating asymmetric hybrid at equilibrium
      Shibayama, N., Morimoto, H., and Saigo, S.
      Biochemistry 36 4375-4381 1997年
    9. Oxygen equilibrium properties of chromium(III)-iron(II) hybrid hemoglobins
      Unzai, S., Hori, H., Miyazaki, G., Shibayama, N., and Morimoto, H.
      Journal of Biological Chemistry 271 12451-12456 1996年
    10. Oxygen equilibrium and electron paramagnetic resonance studies on copper(II)-iron(II) hybrid hemoglobins at room temperature
      Shibayama, N. et al.
      FEBS Letters 372 126-130 1995年
    11. Mechanism of ligand binding to Ni(II)-Fe(II) hybrid hemoglobins
      Shibayama, N., Yonetani, T., Regan, R. M., and Gibson, Q. H.
      Biochemistry 34 14658-14667 1995年
    12. Oxygen equilibrium properties of nickel(II)-iron(II) hybrid hemoglobins cross-linked between 82β1 and 82β2 lysyl residues by bis(3,5-dibromosalicyl)fumarate: Determination of the first two-step microscopic Adair constants for human hemoglobin
      Shibayama, N., Imai, K., Morimoto, H., and Saigo, S.
      Biochemistry 34 4773-4780 1995年
    13. Fixation of the quaternary structures of human adult haemoglobin by encapsulation in transparent porous silica gels
      Shibayama, N., and Saigo, S.
      Journal of Molecular Biology 251 203-209 1995年
    14. 大学物理教育をめぐって その2 医歯薬系の基礎物理 自治医科大学における物理学の新しい教育課程
      青野修, 西郷敏, 原田三男, 柴山修哉
      物理教育 42(3) 307-310 1994年09月
    15. X-ray absorption spectroscopic studies of a transient intermediate in the reaction of cyanide metmyoglobin with dithionite by using rapid freezing
      Saigo, S., Hashimoto, H., Shibayama, N., Nomura, M., and Nagamura, T.
      Biochim. Biophys. Acta. 1202 99-106 1993年
    16. Rapid-freeze XAFS characterization of kinetic intermediates of metalloproteins
      Saigo, S., Hashimoto, H., Shibayama, N., Nomura, M., and Nagamura, T.
      Jpn. J. Appl. Phys. 32 538-540 1993年
    17. Oxygen equilibrium properties of asymmetric nickel(II)-iron(II) hybrid hemoglobin
      Shibayama, N., Imai, K., Morimoto, H., and Saigo, S.
      Biochemistry 32 8792-8798 1993年
    18. Polymerization and solubility of Ni(II)-Fe(II) hybrid Hb S
      Adachi, K., Kim, J., and Shibayama, N.
      Biochim. Biophys. Acta. 1079 268-272 1991年
    19. Oxygen equilibrium properties of highly purified human adult hemoglobin cross-linked between 82β1 and 82β2 lysyl residues by bis(3,5-dibromosalicyl)fumarate
      Shibayama, N. et al.
      Biochemistry 30 8158-8165 1991年
  • 1990-
    1. Structure of deoxy-quaternary haemoglobin with liganded β subunits
      Luisi, B., Liddington, B., Fermi, G., and Shibayama, N.
      Journal of Molecular Biology 214 7-14 1990年
    2. Polymerization of partially liganded hemoglobin S
      Adachi, K., Kim, J., and Shibayama, N.
      Sickle Cell Disease 565 356-357 1989年
    3. Structure of haemoglobin in the deoxy quaternary state with ligand bound at the α haems.
      Luisi, B., and Shibayama, N.
      Journal of Molecular Biology 206 723-736 1989年








自治医科大学 生物物理学部門

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栃木県下野市薬師寺3311-1