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＜原著論文／Articles＞
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  1. 小島正樹, 甲斐基文
    機械翻訳の現状と課題—新しい英文和訳法の提唱—,「東京薬科大学研究紀要」27, 23-28 (2024)
  2. Ohnuki, S., Tokishita, S., Kojima, M., Fujiwara, S.
    Effect of chlorpyrifos‐exposure on the expression levels of CYP genes in Daphnia magna and examination of a possibility that an up‐regulated clan 3 CYP, CYP360A8, reacts with pesticides. Environmental Toxicology, 1-13 (2024)
  3. Fujita, K., Ito, M., Irie, M., Harada, K., Fujiwara, N., Ikeda, Y., Yoshioka, H., Yamazaki, T., Kojima, M., Mikami, B., Mayeda, A., Masuda, S.
    Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nature Communications 15, 455 (2024)
  4. Kouchi, Z., Kojima, M.
    A structural network analysis of neuronal ArhGAP21/23 interactors by computational modeling. ACS Omega 8, 19249-19264 (2023)
  5. Kouchi, Z., Kojima, M.
    Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis. Scientific Reports 12, 4325 (2022)
  6. Konno, S., Kobayashi, K., Senda, M., Funai, Y., Seki, Y., Tamai, I., Schäkel, L., Sakata, K., Thanigaimalai, P., Taguchi, A., Taniguchi, A., Gütschow, M., Müller, C., Takeuchi, K., Hirohama, M., Kawaguchi, A., Kojima, M., Senda, T., Shirasaka, Y., Kamitani, W., Hayashi, Y.
    3CL protease inhibitors with an electrophilic arylketone moiety as anti-SARS-CoV-2 agents. J. Med. Chem. 65, 2926–2939 (2022)
  7. Hoshi, M., Shiino, S., Gomi, A., Sakata, K., Konno, S., Hayashi, Y., Kojima, M.
    In silico design of inhibitor against SARS-CoV-2 protease by docking simulation and ADMET prediction. bioimages 29, 11-21 (2021)
  8. 寺林杏理, 東海林暁貴, 小島正樹
    LISPプログラミングによるグラフ理論の諸問題の効率的なアルゴリズム,「東京薬科大学研究紀要」24, 33-37 (2021)
  9. Ikeda, H., Uchida, H., Okubo, Y., Shibata, T., Sasaki, Y., Suzuki, T., Hamada-Uematsu, M., Hamasaki, R., Okuda, K., Yamaguchi, M., Kojima, M., Tanaka, M., Hamada, H., Tahara, H.
    Antibody screening system using an HSV-based probe to identify a novel target for receptor-retargeted oncolytic HSVs. Journal of Virology 95, e01766-20 (2021)
  10. Akiyama, K., Miura, Y., Hayashi, H., Sakata, A., Matsumura, Y., Kojima, M., Tsuchiya, K., Nitta K., Shiizaki, K., Kurosu, H., Kuro-o, M.
    Calciprotein particles regulate fibroblast growth factor-23 expression in osteoblasts. Kidney International 97, 702-712 (2020)
  11. Kato, Y., Kihara, H., Fukui, K., Kojima, M.
    A ternary complex model of Sirtuin4-NAD+-Glutamate dehydrogenase. Comput. Biol. Chem. 74, 94-104 (2018)
  12. Shojima, T., Hou, F., Takahashi, Y., Matsumura, Y., Okai, M., Nakamura, A., Mizuno, K., Inaba, K., Kojima, M., Miyakawa, T., Tanokura, M.
    Crystal structure of a Ca2+-dependent regulator of flagellar motility reveals the open-closed structural transition. Scientific Reports 8, 2014 (2018)
  13. Sekino, S., Kashiwagi, Y., Kanazawa, H., Takada, K., Baba, T., Sato, S., Inoue, H., Kojima, M., Tani, K.
    The NESH/Abi-3-based WAVE2 complex is functionally distinct from the Abi-1 based WAVE2 complex. Cell Commnunication and Signalling 13, 41 (2015)
  14. Koizumi, T., Terada, T., Nakajima, K., Kojima, M., Koshiba, S., Matsumura, Y., Kaneda, K., Asakura, T., Shimizu-Ibuka, A., Abe, K., Misaka, T.
    Identification of key neoculin residues responsible for the binding and activation of the sweet taste receptor. Scientific Reports 5, 12947 (2015)
  15. Nishii, W., Kukimoto-Niino, M., Terada, T., Shirouzu, M., Muramatsu, T., Kojima, M., Kihara, H., Yokoyama, S.
    A redox switch shapes the Lon protease exit pore to facultively regulate proteolysis. Nature Chemical Biology 11, 46-51 (2015)
  16. Abe, T., Kojima, M., Akanuma, S., Iwashita, H., Yamazaki, T., Okuyama, R., Ichikawa, K., Umemura, M., Nakano, H., Takahashi, S., Takahashi, Y.
    N-terminal hydrophobic amino acids of ATF5 confer IL-1β-induced stabilization. J. Biol. Chem. 289, 3888-3900 (2014)
  17. Shimotakahara, S., Matsui, M., Sakuma, C., Takahashi, T., Fujimoto, T., Furihata, K., Kojima, M., Seino, S., Machinami, T., Shibusawa, Y., Ueda, K. Tashiro, M.
    Dopamine cannot promote oligomerization of unoxidized α-synuclein. J. Biophys. Chem. 4, 110-114 (2013)
  18. Morimoto, Y., Nakagawa, T., Kojima, M.
    Small-angle X-ray scattering constraints and local geometry like secondary structures can construct a coarse-grained protein model at amino acid residue resolution. Biochem. Biophys. Res. Commun. 431, 65-69 (2013)
  19. Sasaki, H., Kubota, K., Lee, W.C., Ohtsuka, J., Kojima, M., Iwata, S., Nakagawa, W., Takahashi, K., Tanokura, M.
    The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis. J. Biochem. 152, 45-52 (2012)
  20. 森本康幹, 中川隆司, 小島正樹
    SAXS法によるタンパク質立体構造の計算科学的解析，「生物物理」 51, 88-91 (2011)
  21. Kezuka, Y., Kojima, M., Mizuno, R., Suzuki, K., Watanabe, T., Nonaka, T.
    Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins 78, 2295-2305 (2010)
  22. Nakanishi-Matsui, M., Kashiwagi, S., Kojima, M., Nonaka, T., Futai, M.
    Roles of the β subunit hinge domain in ATP synthase F1 sector: Hydrophobic network formed by introduced βPhe174 inhibits subunit rotation. Biochem. Biophys. Res. Commun. 395, 173-177 (2010)
  23. Kogo, H., Takeuchi, K., Inoue, H., Kihara, H., Kojima, M., and Takahashi, K.
    Urea-dependent unfolding of HIV-1 protease studied by circular dichroism and small-angle X-ray scattering. Biochim. Biophys. Acta - Proteins and Proteomics 1794, 70-74 (2009)
  24. Kim, Y.-T., Yoshida, H., Kojima, M., Kurita, R., Nishii, W., Muramatsu, T., Ito, H., Park, S.J., and Takahashi, K.
    The effects of mutations in the carboxyl-terminal region on the catalytic activity of Escherichia coli signal peptidase I. J. Biochem. 143, 237-242 (2008)
  25. Kojima, M., Kezuka, Y., Nonaka, T., Hiragi, Y., Watanabe, T., Kimura, K., Takahashi, K., Yanagi, S., and Kihara, H.
    SaxsMDView: A three-dimensional graphics program for displaying force vectors. J. Synchrotron Radiat. 15, 535-537 (2008)
  26. Tashiro, M., Kojima, M., Kihara, H., Kasai, K., Kamiyoshihara, T., Ueda, K., and Shimotakahara, S.
    Characterization of fibrillation process of α-synuclein at the initial stage. Biochem. Biophys. Res. Commun. 369, 910-914 (2008)
  27. Kashiwagi, S., Iwamoto-Kihara, A., Kojima, M., Nonaka, T., Futai, M., and Nakanishi-Matsui, M.
    Effects of mutations in the β subunit hinge domain on ATP synthase F1 sector rotation. Biochem. Biophys. Res. Commun. 365, 227-231 (2007)
  28. Aoki, T., Kojima, M., Tani, K., and Tagaya, M.
    Sec22b-dependent assembly of endoplasmic reticulum Q-SNARE proteins. Biochem. J. 410, 93-100 (2007)
  29. Li, J., Matsumura, Y., Shinjo, M., Kojima, M., and Kihara, H.
    A stable α-helix-rich intermediate is formed by a single mutation of the β-sheet protein, src SH3, at pH 3. J. Mol. Biol. 372, 747-755 (2007)
  30. Huang, X.-P., Yabuki, Y., Kojima, M., Inoue, H., and Takahashi, K.
    Activation profiles of the zymogen of aspergilloglutamic peptidase. Biol. Chem. 388, 129-133 (2007)
  31. Kamiyoshihara, T., Kojima, M., Ueda, K., Tashiro, M., and Shimotakahara, S.
    Observation of multiple intermediates in α-synuclein fibril formation by singular value decomposition analysis. Biochem. Biophys. Res. Commun. 355, 398-403 (2007)
  32. Qin, Q., Inatome, R., Hotta, A., Kojima, M., Yamamura, H., Hirai, H., Yoshizawa, T., Tanaka, H., Fukami, K., and Yanagi, S.
    A novel GTPase, CRAG, mediates promyelocytic leukemia protein-associated nuclear body formation and degradation of expanded polyglutamine protein. J. Cell. Biol. 172, 497-504 (2006)
  33. Hatano, K., Kojima, M., and Tanokura, M.
    Effects of ionization on chemical shifts of the surrounding protons of bromelain inhibitor VI. Proc. Japan. Acad. B 81, 454-458 (2005)
  34. Sasaki, H., Kojima, M., Sawano, Y., Kubota, K., Sunaguma, M., Muramatsu, T., Takahashi, K., and Tanokura, M.
    A proposed catalytic mechanism of aspergilloglutamic peptidase from Aspergillus niger. Proc. Japan. Acad. B 81, 441-446 (2005)
  35. Goda, S., Kojima, M., Nishikawa, Y., Kujo, C., Kawakami, R., Kuramitsu, S, Sakuraba, H., Hiragi, Y., and Ohshima, T.
    Intersubunit interaction induced by subunit rearrangement is essential for the catalytic activity of the hyperthermophilic glutamate dehydrogenase from Pyrobaculum islandicum. Biochemistry 44, 15304-15313 (2005)
  36. Kubota, K., Nishii, W., Kojima, M., and Takahashi, K.
    Specific inhibition and stabilization of aspergilloglutamic peptidase by the propeptide: identification of critical sequences and residues in the propeptide. J. Biol. Chem. 280, 999-1006 (2005)
  37. Sasaki, H., Nakagawa, A., Muramatsu, T., Suganuma, M., Sawano, Y., Kojima, M., Kubota, K., Takahashi, K., and Tanokura, M.
    The three-dimensional structure of aspergilloglutamic peptidase from Aspergillus niger. Proc. Japan Acad. B 80, 435-438 (2004)
  38. Matsuura, H., Shimotakahara, S., Sakuma, C., Tashiro, M., Shindo, H., Mochizuki, K., Yamagishi, A., Kojima, M., and Takahashi, K.
    Thermal unfolding of ribonuclease T1 studied by multi-dimensional NMR spectroscopy. Biol. Chem. 385, 1157-1164 (2004)
  39. Yabuki, Y., Kubota, K., Kojima, M., Inoue H., and Takahashi, K.
    Identification of a glutamine residue essential for catalytic activity of aspergilloglutamic peptidase by site-directed mutagenesis. FEBS Lett. 569, 161-164 (2004)
  40. Kim, Y.-T., Kurita, R., Kojima, M., Nishii, W., Tanokura, M., Muramatsu, T., Ito, H., and Takahashi, K.
    Identification of arginine residues important for the activity of Escherichia coli signal peptidase I. Biol. Chem. 385, 381-388 (2004)
  41. Athauda, S.B.P., Matsumoto, K., Rajapakshe, S., Kuribayashi, M., Kojima, M., Kubomura-Yoshida, N., Iwamatsu, A., Shibata, C., Inoue, H., and Takahashi, K.
    Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases. Biochem. J. 381, 295-306 (2004)
  42. Kojima, M., Timchenko, A.A., Higo, J., Ito, K., Kihara, H., and Takahashi, K.
    Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule. J. Appl. Crystallogr. 37, 103-109 (2004)
  43. Zhu, L., Kihara, H., Kojima, M., Zhou, J.-M., and Perrett, S.
    Small-angle X-ray scattering study of the yeast prion Ure2p. Biochem. Biophys. Res. Commun. 311, 525-532 (2003)
  44. Hatano, K., Kojima, M., Suzuki, E., Tanokura, M., and Takahashi, K.
    Determination of the NMR structure of Gln25-ribonuclease T1. Biol. Chem. 384, 1173-1183 (2003)
  45. Nishii, W., Ueki, T., Miyashita, R., Kojima, M., Kim, Y.-T., Sasaki, N., Murakami-Murofushi, K., and Takahashi, K.
    Structural and enzymatic characterization of physarolisin (formerly physaropepsin) proves that it is a unique serine-carboxyl proteinase. Biochem. Biophys. Res. Commun. 301, 1023-1029 (2003)
  46. Maeda, M., Takeuchi, K., Kojima, M., Tanokura, M., Kimura, K., Amemiya, Y., Kihara, H., and Takahashi, K.
    Kinetic studies of unfolding process of aspergillopepsin II by pH-jump methods. Biochem. Biophys. Res. Commun. 301, 745-750 (2003)
  47. Hatano, K., Kojima, M., Tanokura, M., and Takahashi, K.
    Nuclear magnetic resonance studies on the pKa values and interactions of ionizable groups in bromelain inhibitor VI from pineapple stem. Biol. Chem. 384, 83-91 (2002)
  48. Kojima, M., Tokishita, S., Yamazaki, K., Yamagata, H., and Takahashi, K.
    Molecular modeling of a single-chain immunoglobulin fragment Fab in silico. bioimages 9, 117-122 (2001)
  49. Huang, X.-P., Kagami, N., Inoue, H., Kojima, M., Kimura, T., Makabe, O., Suzuki, K., and Takahashi, K.
    Identification of a glutamic acid and an aspartic acid residue essential for catalytic activity of aspergillopepsin II, a non-pepsin type acid proteinase. J. Biol. Chem. 275, 26607-26614 (2000)
  50. Fujino, T., Kojima, M., Beppu, M., Kikugawa, K., Yasuda, H. , and Takahashi, K.
    Identification of the cleavage sites of oxidized protein that are susceptible to oxidized protein hydrolase (OPH) in the primary and tertiary structures of the protein. J. Biochem. 127, 1087-1093 (2000)
  51. Kojima, M., Tanokura, M., Maeda, M., Kimura, K., Amemiya, Y., Kihara, H., and Takahashi, K.
    pH-dependent unfolding of aspergillopepsin II studied by small-angle X-ray scattering. Biochemistry 39, 1364-1372 (2000)
  52. Hatano, K., Kojima, M., Tanokura, M., and Takahashi, K.
    Solution structure of bromelain inhibitor VI from pineapple stem: structural similarity with Bowman-Birk trypsin/chymotrypsin inhibitor from soybean. Biochemistry 35, 5379-5384 (1996)
  53. Suzuki, R., Kojima, M., and Tanokura, M.
    The relationship between thermodynamic stability and molecular structure of Lys25-ribonuclease T1. bioimages 3, 65-69 (1995)
  54. Kojima, M., Miyano, H., Suzuki, E., Tanokura, M., and Takahashi, K.
    Effects of replacement of Lys25 with Gln on the conformation of ribonuclease T1: sequence-specific 1H-NMR resonance assignments of Gln25 ribonuclease T1 by two dimensional NMR spectroscopy. J. Biochem. 118, 710-716 (1995)
  55. Hatano, K., Kojima, M., Tanokura, M., and Takahashi, K.
    Primary structure, sequence-specific 1H-NMR assignments and secondary structure in solution of bromelain inhibitor VI from pineapple stem. Eur. J. Biochem. 232, 335-343 (1995)
  56. Fukada, H., Takahashi, K., Sorai, M., Kojima, M., Tanokura, M., and Takahashi, K.
    Differential scanning calorimetric studies on the thermal unfolding of acid proteinase A from Aspergillus niger at various pHs. Thermochim. Acta 267, 373-378 (1995)
  57. Kojima, M., Mizukoshi, T., Miyano, H., Suzuki, E., Tanokura, M., and Takahashi, K.
    Thermal stabilization of ribonuclease T1 by carboxymethylation at Glu-58 as revealed by 1H nuclear magnetic resonance spectroscopy. FEBS Lett 351, 389-392 (1994)
  58. Kojima, M., Tanokura, T., Murakami, T., and Takahashi, K.
    Role of glutamic acid-58 of ribonuclease T1 in enzyme action as studied by molecular dynamics simulation of aspartic acid-58 and alanine-58 mutants. bioimages 2, 53-57 (1994)

＜総説／Reviews＞

  1. 小島正樹、松村義隆
    タンパク質変性データの熱力学的解析，「東京薬科大学研究紀要」 26, 74-78 (2023)
  2. 野口瑶、森河良太、西田洋平、野口航、小島正樹、高須昌子
    生命科学部における情報科学およびデータサイエンス教育について，「東京薬科大学研究紀要」 25, 77-84 (2022)
  3. 小島正樹、石塚海帆
    downhill simplex法による非線形最小二乗法について，「東京薬科大学研究紀要」 25, 116-120 (2022)
  4. 小島正樹
    対面授業を超えたオンライン授業を目指して，「とうやく（東京薬科大学東薬会会報）」 420, 18-20 (2021)
  5. 松村義隆、小島正樹
    βグルカン構造予測への計算科学的アプローチ，「βグルカンの基礎研究と応用・利用の動向」 pp. 39-45. シーエムシー出版（2018）
  6. 高須昌子、小島正樹
    正十二面体上のランダムウォークに関する入試問題のコンピュータによる検証，「東京薬科大学研究紀要」 21, 55-60 (2018)
  7. 小島正樹
    生命科学部数学教育における教務支援の自動化，「東京薬科大学研究紀要」 15, 63-67 (2011)
  8. 小島正樹
    数学のある風景，「とうやく（東京薬科大学東薬会会報）」 390, 28-30 (2011)
  9. 小島正樹、野中孝昌、森本康幹、中川隆司、柳茂、木原裕
    NMRとX線溶液散乱データから得られる構造情報の加算性、冗長性、相補性，「日本結晶学会誌」 51, 92-93 (2009)
  10. Goda, S., Kojima, M., Sakuraba, H., Hiragi, Y., and Oshima, T.
    Elucidation of the structural change of interactive misarranged recombinant hyperthermophilic glutamate dehydrogenase during heat induced activation under high temperature, Photon Factory Activity Report A 23, 56-57 (2006)
  11. 小島正樹
    X線溶液散乱法によるタンパク質の立体構造解析，「生化学」 78 (No. 9), 871-874 (2006)
  12. 小島正樹，田代櫻子，神藤平三郎
    直積演算子（product operator）に基づく多次元NMRの測定原理，「東京薬科大学研究紀要」6, 1-9 (2003)
  13. 小島正樹
    タンパク質の折れ畳み過程における非天然様二次構造の形成，「化学と工業」54 (No. 12)，1394 (2001)
  14. Kojima, M., Tanokura, M., and Takahashi, K.
    Structure-function relationship of ribonuclease T1 based on molecular structure. bioimages 8, 45-55 (2000)
  15. 小島正樹
    X線小角散乱法による蛋白質の構造解析，「バイオイメージング技術の最先端」（石川春律監修）pp. 75-79，先端医療技術研究所（1999)
  16. Miyata, N., Yamakoshi, Y., Inoue, H., Kojima, M., Takahashi, K., and Iwata, N.
    Mechanistic study of the inhibition of glutathione S-transferase by C60, in “Fullerenes: Recent Advances in the Chemistry and Physics of Fullerenes and Related Materials, Volume 6” (Kadish, K.M., and Ruoff, R.S. eds.) pp. 1227-1235 The Electrochemical Society, Pennington (1998)
  17. Takahashi, K., Kagami, N., Huang, X.-P., Kojima, M., and Inoue, H.
    Aspergillus niger acid proteinase A. Structure and function. Adv. Exp. Med. Biol. 436, 275-282 (1998)
  18. 田之倉優，小島正樹
    分子構造と機能，「蛋白質　核酸　酵素」42, 961-962 (1997)
  19. 鈴木倫太郎，小島正樹，田之倉優
    分子構造表示ソフトInsightII–リボヌクレアーゼT1への応用–，「先端医療」3, 3-7 (1996)

＜著書,訳書／Books＞

  1. 小島正樹（共訳）
    「改訂版　理系研究者のためのアカデミックライティング」（ヒラリー・グラスマン-ディール著），東京図書 (2023)
  2. 小島正樹
    「薬学のための統計教科書」東京図書 （2015）
  3. 小島正樹（共訳）
    「ドラッグデザイン―構造とリガンドに基づくアプローチ」（Merz, Ringe, Reynolds編，田之倉優，小島正樹監訳），東京化学同人 （2014）
  4. 小島正樹
    「化学・生命科学のための線形代数」東京化学同人 (2012)
  5. 小島正樹（共訳）
    「理系研究者のためのアカデミックライティング」（ヒラリー・グラスマン-ディール著），東京図書 (2011)
  6. 小島正樹（分担執筆）
    「未来の治療に向かって―生命医科学の挑戦」（多賀谷光男，柳茂編），東京化学同人 (2010)
  7. 小島正樹，田之倉優（分担執筆）
    「生物物理学ハンドブック」（石渡信一，桂勲，桐野豊，美宅成樹編），朝倉書店 (2007)
  8. 小島正樹（共訳）
    「物理生化学」（van Holde, Johnson, Ho著，田之倉優，有坂文雄監訳），医学出版 （2002）
  9. 小島正樹（分担執筆）
    「ライフサイエンス基礎実験」（水島昭二，大島泰郎，高橋健治，三浦卓編），丸善 (1996)