Details of the Researcher

PHOTO

Misaki Kinoshita
Section
Frontier Research Institute for Interdisciplinary Sciences
Job title
Specially Appointed Assistant Professor(Research)
Degree
e-Rad No.
10823809

Research History 4

  • 2026/04 - Present
    東北大学 学際科学フロンティア研究所　特任助教

  • 2021/04 - 2026/03
    一般社団法人 日本血液製剤機構

  • 2020/08 - 2021/03
    バイオ科学株式会社

  • 2018/04 - 2019/12
    Tohoku University　Frontier Research Institute for Interdisciplinary Sciences

Education 3

  • 大阪大学大学院　理学研究科　生物科学専攻

    2015/04 - 2018/03

  • 大阪大学大学院　理学研究科　生物科学専攻

    2013/04 - 2015/03

  • Osaka University　School of Science

    2009/04 - 2013/03

Professional Memberships 3

  • THE BIOPHYSICAL SOCIETY OF JAPAN

  • PROTEIN SCIENCE SOCIETY OF JAPAN

  • THE JAPANESE BIOCHEMICAL SOCIETY

Research Interests 5

  • Fluorescence

  • Numerical acalysis

  • Amyloid

  • Isotermal titration calorimetry

  • interprotein interaction

Research Areas 2

  • Life sciences / Biophysics / protein aggregation

  • Life sciences / Structural biochemistry / ER chaperone

Papers 20

  1. De novo design of a peptide ligand for specific affinity purification of human complement C1q

    Ryo Tsuchihashi, Misaki Kinoshita, Hiroaki Aino

    2026/04/01

    Publisher: openRxiv

    DOI： 10.64898/2026.03.30.714096 　

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    Abstract Affinity purification is a essential technique for isolating highly purified proteins; however, generating affinity ligands require significant time and financial investment. To address these limitations, this study proposes a novel affinity chromatography method utilizing in silico -designed cyclic peptides as ligands. Targeting Complement C1q (C1q), a plasma protein that plays crucial roles in classical complement pathway, we employed the biomolecular structure prediction model, AlphaFold2, to design specific binding cyclic peptides. Based on these designs, we synthesized lariat-type cyclic peptides characterized by disulfide cyclization and biotinylation, which were subsequently immobilized on streptavidin carriers. Performance tests confirmed that the resulting column specifically captured C1q, allowing for elution via a standard NaCl concentration gradient. Notably, high selectivity was preserved even in the presence of plasma, underscoring the ligand’s practical robustness. By overcoming traditional constraints through (1) rapid and simple design, (2) high specificity, and (3) universal versatility without genetic modification, this de novo design strategy represents a potential breakthrough in protein purification technologies. Highlights AI-driven de novo design generated a specific cyclic peptide ligand for Complement C1q The synthetic ligand enabled one-step purification of Complement C1q directly from human plasma Mild elution conditions preserved the target’s oligomeric structure and native interactome This label-free strategy offers a rapid, low-cost alternative to antibody-based chromatography

  2. Cyclic peptides space: The methodology of sequence selection to cover the comprehensive physical properties

    Ryo Tsuchihashi, Misaki Kinoshita

    2026/03/12

    Publisher: openRxiv

    DOI： 10.64898/2026.03.10.710724 　

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    Abstract Cyclic peptides have emerged as a pivotal modality for next-generation therapeutics, due to their superior biocompatibility, high selectivity, and structural stability. While AI-driven peptide design has advanced rapidly, conventional optimization algorithms are often constrained by initialization biases, which impede the efficient exploration of the vast chemical space. Here, we propose a novel methodology that integrates the protein language model ESM-2 with cyclic permutation averaging of embeddings to resolve this bottleneck. This approach establishes a comprehensive "peptide space", a high-dimensional vector representation that encapsulates the physicochemical and structural attributes of cyclic peptides. Our analysis reveals that random sequence selection results in a heterogeneous distribution within this space, potentially underrepresenting specific functional regions. Conversely, navigating this defined peptide space enables the selection of libraries that uniformly span diverse molecular properties. In a proof-of-concept study designing binders for β2-microglobulin (β2m), we demonstrate that initial sequences uniformly sampled from our peptide space yield superior candidates more efficiently than those derived from random selection. Furthermore, this framework facilitates the quantitative assessment of mutational perturbations on global peptide properties, supporting rational decision-making for both broad exploration and local optimization. This "peptide space" concept provides a foundational framework for defining appropriate search boundaries and enhancing computational efficiency in AI-mediated drug discovery. Graphic Abstract

  3. A unique leucine-valine adhesive motif supports structure and function of protein disulfide isomerase P5 via dimerization

    Masaki Okumura, Shingo Kanemura, Motonori Matsusaki, Misaki Kinoshita, Tomohide Saio, Dai Ito, Chihiro Hirayama, Hiroyuki Kumeta, Mai Watabe, Yuta Amagai, Young-Ho Lee, Shuji Akiyama, Kenji Inaba

    Structure　2021/04

    Publisher: Elsevier BV

    DOI： 10.1016/j.str.2021.03.016 　

    ISSN： 0969-2126

  4. Antipsychotic olanzapine-induced misfolding of proinsulin in the endoplasmic reticulum accounts for atypical development of diabetes. International-journal

    Satoshi Ninagawa, Seiichiro Tada, Masaki Okumura, Kenta Inoguchi, Misaki Kinoshita, Shingo Kanemura, Koshi Imami, Hajime Umezawa, Tokiro Ishikawa, Robert B Mackin, Seiji Torii, Yasushi Ishihama, Kenji Inaba, Takayuki Anazawa, Takahiko Nagamine, Kazutoshi Mori

    eLife　9　2020/11/17

    DOI： 10.7554/eLife.60970 　

    ISSN： 2050-084X

  5. The protein disulfide isomerase family: from proteostasis to pathogenesis Peer-reviewed

    Matsusaki, M, Kanemura, S, Kinoshita, M, Lee, Y.H, Inaba, K, Okumura, M

    Biochem. Biophys. Acta. General Subject　2020/01

  6. Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40). Peer-reviewed

    Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH

    ACS nano　2019/07

    DOI： 10.1021/acsnano.9b01578 　

    ISSN： 1936-0851

  7. Dynamic assembly of protein disulfide isomerase in catalysis of oxidative folding

    Masaki Okumura, Kentaro Noi, Shingo Kanemura, Misaki Kinoshita, Tomohide Saio, Yuichi Inoue, Takaaki Hikima, Shuji Akiyama, Teru Ogura, Kenji Inaba

    Nature Chemical Biology　15　(5)　499-509　2019/05

    Publisher: Springer Science and Business Media LLC

    DOI： 10.1038/s41589-019-0268-8 　

    ISSN： 1552-4450

    eISSN： 1552-4469

  8. Zinc boosts EGCG's hIAPP amyloid Inhibition both in solution and membrane. Peer-reviewed

    Lee YH, Lin Y, Cox SJ, Kinoshita M, Sahoo BR, Ivanova M, Ramamoorthy A

    Biochimica et biophysica acta. Proteins and proteomics　2018/11

    DOI： 10.1016/j.bbapap.2018.11.006 　

    ISSN： 1570-9639

  9. Graphene quantum dots prevent α-synucleinopathy in Parkinson's disease Peer-reviewed

    Kim D, Yoo JM, Hwang H, Lee J, Lee SH, Yun SP, Park MJ, Lee M, Choi S, Kwon SH, Lee S, Kwon SH, Kim S, Park YJ, Kinoshita M, Lee YH, Shin S, Paik SR, Lee SJ, Lee S, Hong BH, Ko HS

    Nat. Nanotechnol.　2018/07

    DOI： 10.1038/s41565-018-0179-y 　

    ISSN： 1748-3387

  10. Energy landscape of polymorphic amyloid generation of β2-microglobulin revealed by calorimetry Peer-reviewed

    Kinoshita M, Lin Y, Dai I, Okumura M, Markova N, Ladbury JE, Sterpone F, Lee YH, These authors contributed equally to this wor

    Chem. Commun. (Camb).　54　(57)　7995-7998　2018/07

    DOI： 10.1039/c8cc02718h 　

    ISSN： 1359-7345

  11. Impact of membrane curvature on amyloid aggregation. Peer-reviewed

    Terakawa MS, Lin Y, Kinoshita M, Kanemura S, Itoh D, Sugiki T, Okumura M, Ramamoorthy A, Lee YH

    Biochimica et biophysica acta. Biomembranes　2018/04

    DOI： 10.1016/j.bbamem.2018.04.012 　

    ISSN： 0006-3002

  12. Membrane-induced initial structure of α-synuclein control its amyloidogenesis on model membranes Peer-reviewed

    Mayu S. Terakawa, Young-Ho Lee, Misaki Kinoshita, Yuxi Lin, Toshihiko Sugiki, Naoya Fukui, Tatsuya Ikenoue, Yasushi Kawata, Yuji Goto

    Biochimica et Biophysica Acta - Biomembranes　1860　(3)　757-766　2018/03/01

    Publisher: Elsevier B.V.

    DOI： 10.1016/j.bbamem.2017.12.011 　

    ISSN： 1879-2642 0005-2736

  13. Kinetics and polymorphs of yeast prion Sup35NM amyloidogenesis Peer-reviewed

    Misaki Kinoshita, Yuxi Lin, Masatoshi Nakatsuji, Takashi Inui, Young-Ho Lee

    INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES　102　1241-1249　2017/09

    DOI： 10.1016/j.ijbiomac.2017.05.001 　

    ISSN： 0141-8130

    eISSN： 1879-0003

  14. Model membrane size-dependent amyloidogenesis of Alzheimer's amyloid-beta peptides Peer-reviewed

    Misaki Kinoshita, Erina Kakimoto, Mayu S. Terakawa, Yuxi Lin, Tatsuya Ikenoue, Masatomo So, Toshihiko Sugiki, Ayyalusamy Ramamoorthy, Yuji Goto, Young-Ho Lee

    PHYSICAL CHEMISTRY CHEMICAL PHYSICS　19　(24)　16257-16266　2017/06

    DOI： 10.1039/c6cp07774a 　

    ISSN： 1463-9076

    eISSN： 1463-9084

  15. Energetic basis on interactions between ferredoxin and ferredoxin NADP(+) reductase at varying physiological conditions Peer-reviewed

    Misaki Kinoshita, Ju Yaen Kim, Satoshi Kume, Yuxi Lin, K. Hun Mok, Yosky Kataoka, Koichiro Ishimori, Natalia Markova, Genji Kurisu, Toshiharu Hase, Young-Ho Lee

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS　482　(4)　909-915　2017/01

    DOI： 10.1016/j.bbrc.2016.11.132 　

    ISSN： 0006-291X

    eISSN： 1090-2104

  16. Non-covalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity Peer-reviewed

    Ju Yaen Kim, Misaki Kinoshita, Satoshi Kume, G. T. Hanke, Toshihiko Sugiki, John E. Ladbury, Chojiro Kojima, Takahisa Ikegami, Genji Kurisu, Yuji Goto, Toshiharu Hase, Young-Ho Lee

    BIOCHEMICAL JOURNAL　473　(21)　3837-3854　2016/11

    DOI： 10.1042/BCJ20160658 　

    ISSN： 0264-6021

    eISSN： 1470-8728

  17. A thiirane linker for isopeptide mimetics by peptide ligation Peer-reviewed

    Toru Kawakami, Yuichi Mishima, Misaki Kinoshita, Young-Ho Lee, Isao Suetake

    TETRAHEDRON LETTERS　57　(19)　2112-2115　2016/05

    DOI： 10.1016/j.tetlet.2016.04.006 　

    ISSN： 0040-4039

  18. Amorphous Aggregation of Cytochrome c with Inherently Low Amyloidogenicity Is Characterized by the Metastability of Supersaturation and the Phase Diagram Peer-reviewed

    Yuxi Lin, Jozsef Kardos, Mizue Imai, Tatsuya Ikenoue, Misaki Kinoshita, Toshihiko Sugiki, Koichiro Ishimori, Yuji Goto, Young-Ho Lee

    LANGMUIR　32　(8)　2010-2022　2016/03

    DOI： 10.1021/acs.langmuir.5b03810 　

    ISSN： 0743-7463

  19. Physicochemical natures of interfaces control activity of ferredoxin NADP+ reductase through its interprotein interactions with ferredoxin Peer-reviewed

    Misaki Kinoshita, Ju yaen Kim, Satoshi Kume, Yukiko Sakakibara, Toshihiko Sugiki, Chojiro Kojima, Genji Kurisu, Takahisa Ikegami, Toshiharu Hase, Yoko Kimata-Ariga, Young-Ho Lee

    BBA - Bioenergetics　1847　(10)　1200-1211　2015/10

    Publisher: ELSEVIER

    DOI： 10.1016/j.bbabio.2015.05.023 　

    ISSN： 0005-2728

  20. Physicochemical nature of interfaces controlling ferredoxin NADP(+) reductase activity through its interprotein interactions with ferredoxin. International-journal Peer-reviewed

    Kinoshita M, Kim JY, Kume S, Sakakibara Y, Sugiki T, Kojima C, Kurisu G, Ikegami T, Hase T, Kimata-Ariga Y, Lee YH

    Biochimica et biophysica acta　1847　(10)　1200-1211　2015/10

    DOI： 10.1016/j.bbabio.2015.05.023 　

    ISSN： 0006-3002

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    Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP(+) reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We herein demonstrated that intermolecular hydrophobic and charge-charge interactions between Fd and enzymes were both critical for enzymatic activity. Systematic site-directed mutagenesis, which altered physicochemical properties of residues on the interfaces of Fd for FNR /SiR, revealed various changes in activities of both enzymes. The replacement of serine 43 of Fd to a hydrophobic residue (S43W) and charged residue (S43D) increased and decreased FNR activity, respectively, while S43W showed significantly lower SiR activity without affecting SiR activity by S43D, suggesting that hydrophobic and electrostatic interprotein forces affected FNR activity. Enzyme kinetics revealed that changes in FNR activity by mutating Fd correlated with Km, but not with kcat or activation energy, indicating that interprotein interactions determined FNR activity. Calorimetry-based binding thermodynamics between Fd and FNR showed different binding modes of FNR to wild-type, S43W, or S43D, which were controlled by enthalpy and entropy, as shown by the driving force plot. Residue-based NMR spectroscopy of (15)N FNR with Fds also revealed distinct binding modes of each complex based on different directions of NMR peak shifts with similar overall chemical shift differences. We proposed that subtle adjustments in both hydrophobic and electrostatic forces were critical for enzymatic activity, and these results may be applicable to protein-based electron transfer systems.

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Misc. 9

  1. Impact of membrane curvature on amyloid aggregation Peer-reviewed

    Mayu S. Terakawa, Yuxi Lin, Misaki Kinoshita, Shingo Kanemura, Dai Itoh, Toshihiko Sugiki, Masaki Okumura, Ayyalusamy Ramamoorthy, Young-Ho Lee

    Biochimica et Biophysica Acta - Biomembranes　2018

    Publisher: Elsevier B.V.

    DOI： 10.1016/j.bbamem.2018.04.012 　

    ISSN： 1879-2642 0005-2736

  2. Biochemical and biophysical methods to examine the effects of site-directed mutagenesis on enzymatic activities and interprotein interactions Peer-reviewed

    Misaki Kinoshita, Ju Yaen Kim, Yuxi Lin, Natalia Markova, Toshiharu Hase, Young-Ho Lee

    Methods in Molecular Biology　1498　439-460　2017

    Publisher: Humana Press Inc.

    DOI： 10.1007/978-1-4939-6472-7_30 　

    ISSN： 1064-3745

  3. Thermodynamics of protein-protein interactions examined by isothermal titration calorimetery Invited Peer-reviewed

    Kim JY, Kinoshita M, Lin Y, Lee YH

    Biochemistry Research Trends, Protein-Protein interactions　67-80　2017

  4. Molecular structure of amyloid fibrils revealed by thermodynamics Invited Peer-reviewed

    Ikenoue T, Lin Y, Kinoshita M, Sakurai K, Goto Y, Lee YH

    Biochemistry Research Trends, Protein-Protein interactions　81-96　2017

  5. Practical tips for MicroCal PEAQ-ITC experiments: troubleshooting and additional help to maximize performance Invited Peer-reviewed

    Kinoshita M, Kim JY, Lin Y, Lee YH

    Malvern Technical note, Malvern Instrument Ltd.　2017

  6. Biophysical application of calorimetric methods to protein misfolding and aggregation examinations Invited Peer-reviewed

    Ikenoue T, Kinoshita M, Lin Y, Lee YH

    White paper (Malvern Instrument Ltd.)　2017

  7. チイランリンカーを用いるイソペプチド類似構造を介したヒストンペプチドのユビキチン化

    川上徹, 三島優一, 木下岬, 李映昊, 末武勲, 末武勲

    日本生化学会大会(Web)　89th　2016

  8. Ubiquitination of Histone Peptides via Isopeptide Mimetics by Using a Thiirane Linker

    KAWAKAMI Toru, MISHIMA Yuichi, KINOSHITA Misaki, LEE Young-Ho, SUETAKE Isao, SUETAKE Isao

    Peptide Science　2016　2016

    ISSN： 1344-7661

  9. Delicate Balance of Noncovalent Forces Control the Electron Transfer Complex between Ferredoxin and Sulfite Reductase to Optimize Enzymatic Activity

    Juyaen Kim, Misaki Kinoshita, Takahisa Ikegami, Genji Kurisu, Yuji Goto, Toshiharu Hase, Young-Ho Lee

    PROTEIN SCIENCE　24　64-65　2015/10

    ISSN： 0961-8368

    eISSN： 1469-896X

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Presentations 1

  1. Physicochemical nature of interfaces controlling ferredoxin NADP+ reductase activity through its interprotein interactions with frredoxin International-presentation

    Kinoshita M, Kim JY, Sugiki T, Kojima C, KUrisu G, Ikegami T, Ariga YK, Hase T, Lee YH

    International Conference on Magnetic Resonance in Biological Systems　2016